1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsc/private/hashseti.h> 3 4 PetscClassId PETSCPARTITIONER_CLASSID = 0; 5 6 PetscFunctionList PetscPartitionerList = NULL; 7 PetscBool PetscPartitionerRegisterAllCalled = PETSC_FALSE; 8 9 PetscBool ChacoPartitionercite = PETSC_FALSE; 10 const char ChacoPartitionerCitation[] = "@inproceedings{Chaco95,\n" 11 " author = {Bruce Hendrickson and Robert Leland},\n" 12 " title = {A multilevel algorithm for partitioning graphs},\n" 13 " booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing (CDROM)}," 14 " isbn = {0-89791-816-9},\n" 15 " pages = {28},\n" 16 " doi = {http://doi.acm.org/10.1145/224170.224228},\n" 17 " publisher = {ACM Press},\n" 18 " address = {New York},\n" 19 " year = {1995}\n}\n"; 20 21 PetscBool ParMetisPartitionercite = PETSC_FALSE; 22 const char ParMetisPartitionerCitation[] = "@article{KarypisKumar98,\n" 23 " author = {George Karypis and Vipin Kumar},\n" 24 " title = {A Parallel Algorithm for Multilevel Graph Partitioning and Sparse Matrix Ordering},\n" 25 " journal = {Journal of Parallel and Distributed Computing},\n" 26 " volume = {48},\n" 27 " pages = {71--85},\n" 28 " year = {1998}\n}\n"; 29 30 /*@C 31 DMPlexCreatePartitionerGraph - Create a CSR graph of point connections for the partitioner 32 33 Input Parameters: 34 + dm - The mesh DM dm 35 - height - Height of the strata from which to construct the graph 36 37 Output Parameter: 38 + numVertices - Number of vertices in the graph 39 . offsets - Point offsets in the graph 40 . adjacency - Point connectivity in the graph 41 - globalNumbering - A map from the local cell numbering to the global numbering used in "adjacency". Negative indicates that the cell is a duplicate from another process. 42 43 The user can control the definition of adjacency for the mesh using DMSetAdjacency(). They should choose the combination appropriate for the function 44 representation on the mesh. 45 46 Level: developer 47 48 .seealso: PetscPartitionerGetType(), PetscPartitionerCreate(), DMSetAdjacency() 49 @*/ 50 PetscErrorCode DMPlexCreatePartitionerGraph(DM dm, PetscInt height, PetscInt *numVertices, PetscInt **offsets, PetscInt **adjacency, IS *globalNumbering) 51 { 52 PetscInt dim, depth, p, pStart, pEnd, a, adjSize, idx, size; 53 PetscInt *adj = NULL, *vOffsets = NULL, *graph = NULL; 54 IS cellNumbering; 55 const PetscInt *cellNum; 56 PetscBool useCone, useClosure; 57 PetscSection section; 58 PetscSegBuffer adjBuffer; 59 PetscSF sfPoint; 60 PetscInt *adjCells = NULL, *remoteCells = NULL; 61 const PetscInt *local; 62 PetscInt nroots, nleaves, l; 63 PetscMPIInt rank; 64 PetscErrorCode ierr; 65 66 PetscFunctionBegin; 67 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 68 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 69 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 70 if (dim != depth) { 71 /* We do not handle the uninterpolated case here */ 72 ierr = DMPlexCreateNeighborCSR(dm, height, numVertices, offsets, adjacency);CHKERRQ(ierr); 73 /* DMPlexCreateNeighborCSR does not make a numbering */ 74 if (globalNumbering) {ierr = DMPlexCreateCellNumbering_Internal(dm, PETSC_TRUE, globalNumbering);CHKERRQ(ierr);} 75 /* Different behavior for empty graphs */ 76 if (!*numVertices) { 77 ierr = PetscMalloc1(1, offsets);CHKERRQ(ierr); 78 (*offsets)[0] = 0; 79 } 80 /* Broken in parallel */ 81 if (rank && *numVertices) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Parallel partitioning of uninterpolated meshes not supported"); 82 PetscFunctionReturn(0); 83 } 84 ierr = DMPlexGetHeightStratum(dm, height, &pStart, &pEnd);CHKERRQ(ierr); 85 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 86 ierr = PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 87 /* Build adjacency graph via a section/segbuffer */ 88 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ion);CHKERRQ(ierr); 89 ierr = PetscSectionSetChart(section, pStart, pEnd);CHKERRQ(ierr); 90 ierr = PetscSegBufferCreate(sizeof(PetscInt),1000,&adjBuffer);CHKERRQ(ierr); 91 /* Always use FVM adjacency to create partitioner graph */ 92 ierr = DMGetBasicAdjacency(dm, &useCone, &useClosure);CHKERRQ(ierr); 93 ierr = DMSetBasicAdjacency(dm, PETSC_TRUE, PETSC_FALSE);CHKERRQ(ierr); 94 ierr = DMPlexCreateCellNumbering_Internal(dm, PETSC_TRUE, &cellNumbering);CHKERRQ(ierr); 95 if (globalNumbering) { 96 ierr = PetscObjectReference((PetscObject)cellNumbering);CHKERRQ(ierr); 97 *globalNumbering = cellNumbering; 98 } 99 ierr = ISGetIndices(cellNumbering, &cellNum);CHKERRQ(ierr); 100 /* For all boundary faces (including faces adjacent to a ghost cell), record the local cell in adjCells 101 Broadcast adjCells to remoteCells (to get cells from roots) and Reduce adjCells to remoteCells (to get cells from leaves) 102 */ 103 ierr = PetscSFGetGraph(dm->sf, &nroots, &nleaves, &local, NULL);CHKERRQ(ierr); 104 if (nroots >= 0) { 105 PetscInt fStart, fEnd, f; 106 107 ierr = PetscCalloc2(nroots, &adjCells, nroots, &remoteCells);CHKERRQ(ierr); 108 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 109 for (l = 0; l < nroots; ++l) adjCells[l] = -3; 110 for (f = fStart; f < fEnd; ++f) { 111 const PetscInt *support; 112 PetscInt supportSize; 113 114 ierr = DMPlexGetSupport(dm, f, &support);CHKERRQ(ierr); 115 ierr = DMPlexGetSupportSize(dm, f, &supportSize);CHKERRQ(ierr); 116 if (supportSize == 1) adjCells[f] = cellNum[support[0]]; 117 else if (supportSize == 2) { 118 ierr = PetscFindInt(support[0], nleaves, local, &p);CHKERRQ(ierr); 119 if (p >= 0) adjCells[f] = cellNum[support[1]]; 120 ierr = PetscFindInt(support[1], nleaves, local, &p);CHKERRQ(ierr); 121 if (p >= 0) adjCells[f] = cellNum[support[0]]; 122 } 123 } 124 for (l = 0; l < nroots; ++l) remoteCells[l] = -1; 125 ierr = PetscSFBcastBegin(dm->sf, MPIU_INT, adjCells, remoteCells);CHKERRQ(ierr); 126 ierr = PetscSFBcastEnd(dm->sf, MPIU_INT, adjCells, remoteCells);CHKERRQ(ierr); 127 ierr = PetscSFReduceBegin(dm->sf, MPIU_INT, adjCells, remoteCells, MPI_MAX);CHKERRQ(ierr); 128 ierr = PetscSFReduceEnd(dm->sf, MPIU_INT, adjCells, remoteCells, MPI_MAX);CHKERRQ(ierr); 129 } 130 /* Combine local and global adjacencies */ 131 for (*numVertices = 0, p = pStart; p < pEnd; p++) { 132 const PetscInt *cone; 133 PetscInt coneSize, c; 134 135 /* Skip non-owned cells in parallel (ParMetis expects no overlap) */ 136 if (nroots > 0) {if (cellNum[p] < 0) continue;} 137 /* Add remote cells */ 138 if (remoteCells) { 139 ierr = DMPlexGetCone(dm, p, &cone);CHKERRQ(ierr); 140 ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); 141 for (c = 0; c < coneSize; ++c) { 142 if (remoteCells[cone[c]] != -1) { 143 PetscInt *PETSC_RESTRICT pBuf; 144 145 ierr = PetscSectionAddDof(section, p, 1);CHKERRQ(ierr); 146 ierr = PetscSegBufferGetInts(adjBuffer, 1, &pBuf);CHKERRQ(ierr); 147 *pBuf = remoteCells[cone[c]]; 148 } 149 } 150 } 151 /* Add local cells */ 152 adjSize = PETSC_DETERMINE; 153 ierr = DMPlexGetAdjacency(dm, p, &adjSize, &adj);CHKERRQ(ierr); 154 for (a = 0; a < adjSize; ++a) { 155 const PetscInt point = adj[a]; 156 if (point != p && pStart <= point && point < pEnd) { 157 PetscInt *PETSC_RESTRICT pBuf; 158 ierr = PetscSectionAddDof(section, p, 1);CHKERRQ(ierr); 159 ierr = PetscSegBufferGetInts(adjBuffer, 1, &pBuf);CHKERRQ(ierr); 160 *pBuf = cellNum[point]; 161 } 162 } 163 (*numVertices)++; 164 } 165 ierr = PetscFree2(adjCells, remoteCells);CHKERRQ(ierr); 166 ierr = DMSetBasicAdjacency(dm, useCone, useClosure);CHKERRQ(ierr); 167 /* Derive CSR graph from section/segbuffer */ 168 ierr = PetscSectionSetUp(section);CHKERRQ(ierr); 169 ierr = PetscSectionGetStorageSize(section, &size);CHKERRQ(ierr); 170 ierr = PetscMalloc1(*numVertices+1, &vOffsets);CHKERRQ(ierr); 171 for (idx = 0, p = pStart; p < pEnd; p++) { 172 if (nroots > 0) {if (cellNum[p] < 0) continue;} 173 ierr = PetscSectionGetOffset(section, p, &(vOffsets[idx++]));CHKERRQ(ierr); 174 } 175 vOffsets[*numVertices] = size; 176 if (offsets) *offsets = vOffsets; 177 ierr = PetscSegBufferExtractAlloc(adjBuffer, &graph);CHKERRQ(ierr); 178 ierr = ISRestoreIndices(cellNumbering, &cellNum);CHKERRQ(ierr); 179 ierr = ISDestroy(&cellNumbering);CHKERRQ(ierr); 180 if (adjacency) *adjacency = graph; 181 /* Clean up */ 182 ierr = PetscSegBufferDestroy(&adjBuffer);CHKERRQ(ierr); 183 ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr); 184 ierr = PetscFree(adj);CHKERRQ(ierr); 185 PetscFunctionReturn(0); 186 } 187 188 /*@C 189 DMPlexCreateNeighborCSR - Create a mesh graph (cell-cell adjacency) in parallel CSR format. 190 191 Collective 192 193 Input Arguments: 194 + dm - The DMPlex 195 - cellHeight - The height of mesh points to treat as cells (default should be 0) 196 197 Output Arguments: 198 + numVertices - The number of local vertices in the graph, or cells in the mesh. 199 . offsets - The offset to the adjacency list for each cell 200 - adjacency - The adjacency list for all cells 201 202 Note: This is suitable for input to a mesh partitioner like ParMetis. 203 204 Level: advanced 205 206 .seealso: DMPlexCreate() 207 @*/ 208 PetscErrorCode DMPlexCreateNeighborCSR(DM dm, PetscInt cellHeight, PetscInt *numVertices, PetscInt **offsets, PetscInt **adjacency) 209 { 210 const PetscInt maxFaceCases = 30; 211 PetscInt numFaceCases = 0; 212 PetscInt numFaceVertices[30]; /* maxFaceCases, C89 sucks sucks sucks */ 213 PetscInt *off, *adj; 214 PetscInt *neighborCells = NULL; 215 PetscInt dim, cellDim, depth = 0, faceDepth, cStart, cEnd, c, numCells, cell; 216 PetscErrorCode ierr; 217 218 PetscFunctionBegin; 219 /* For parallel partitioning, I think you have to communicate supports */ 220 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 221 cellDim = dim - cellHeight; 222 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 223 ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); 224 if (cEnd - cStart == 0) { 225 if (numVertices) *numVertices = 0; 226 if (offsets) *offsets = NULL; 227 if (adjacency) *adjacency = NULL; 228 PetscFunctionReturn(0); 229 } 230 numCells = cEnd - cStart; 231 faceDepth = depth - cellHeight; 232 if (dim == depth) { 233 PetscInt f, fStart, fEnd; 234 235 ierr = PetscCalloc1(numCells+1, &off);CHKERRQ(ierr); 236 /* Count neighboring cells */ 237 ierr = DMPlexGetHeightStratum(dm, cellHeight+1, &fStart, &fEnd);CHKERRQ(ierr); 238 for (f = fStart; f < fEnd; ++f) { 239 const PetscInt *support; 240 PetscInt supportSize; 241 ierr = DMPlexGetSupportSize(dm, f, &supportSize);CHKERRQ(ierr); 242 ierr = DMPlexGetSupport(dm, f, &support);CHKERRQ(ierr); 243 if (supportSize == 2) { 244 PetscInt numChildren; 245 246 ierr = DMPlexGetTreeChildren(dm,f,&numChildren,NULL);CHKERRQ(ierr); 247 if (!numChildren) { 248 ++off[support[0]-cStart+1]; 249 ++off[support[1]-cStart+1]; 250 } 251 } 252 } 253 /* Prefix sum */ 254 for (c = 1; c <= numCells; ++c) off[c] += off[c-1]; 255 if (adjacency) { 256 PetscInt *tmp; 257 258 ierr = PetscMalloc1(off[numCells], &adj);CHKERRQ(ierr); 259 ierr = PetscMalloc1(numCells+1, &tmp);CHKERRQ(ierr); 260 ierr = PetscMemcpy(tmp, off, (numCells+1) * sizeof(PetscInt));CHKERRQ(ierr); 261 /* Get neighboring cells */ 262 for (f = fStart; f < fEnd; ++f) { 263 const PetscInt *support; 264 PetscInt supportSize; 265 ierr = DMPlexGetSupportSize(dm, f, &supportSize);CHKERRQ(ierr); 266 ierr = DMPlexGetSupport(dm, f, &support);CHKERRQ(ierr); 267 if (supportSize == 2) { 268 PetscInt numChildren; 269 270 ierr = DMPlexGetTreeChildren(dm,f,&numChildren,NULL);CHKERRQ(ierr); 271 if (!numChildren) { 272 adj[tmp[support[0]-cStart]++] = support[1]; 273 adj[tmp[support[1]-cStart]++] = support[0]; 274 } 275 } 276 } 277 #if defined(PETSC_USE_DEBUG) 278 for (c = 0; c < cEnd-cStart; ++c) if (tmp[c] != off[c+1]) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Offset %d != %d for cell %d", tmp[c], off[c], c+cStart); 279 #endif 280 ierr = PetscFree(tmp);CHKERRQ(ierr); 281 } 282 if (numVertices) *numVertices = numCells; 283 if (offsets) *offsets = off; 284 if (adjacency) *adjacency = adj; 285 PetscFunctionReturn(0); 286 } 287 /* Setup face recognition */ 288 if (faceDepth == 1) { 289 PetscInt cornersSeen[30] = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}; /* Could use PetscBT */ 290 291 for (c = cStart; c < cEnd; ++c) { 292 PetscInt corners; 293 294 ierr = DMPlexGetConeSize(dm, c, &corners);CHKERRQ(ierr); 295 if (!cornersSeen[corners]) { 296 PetscInt nFV; 297 298 if (numFaceCases >= maxFaceCases) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Exceeded maximum number of face recognition cases"); 299 cornersSeen[corners] = 1; 300 301 ierr = DMPlexGetNumFaceVertices(dm, cellDim, corners, &nFV);CHKERRQ(ierr); 302 303 numFaceVertices[numFaceCases++] = nFV; 304 } 305 } 306 } 307 ierr = PetscCalloc1(numCells+1, &off);CHKERRQ(ierr); 308 /* Count neighboring cells */ 309 for (cell = cStart; cell < cEnd; ++cell) { 310 PetscInt numNeighbors = PETSC_DETERMINE, n; 311 312 ierr = DMPlexGetAdjacency_Internal(dm, cell, PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, &numNeighbors, &neighborCells);CHKERRQ(ierr); 313 /* Get meet with each cell, and check with recognizer (could optimize to check each pair only once) */ 314 for (n = 0; n < numNeighbors; ++n) { 315 PetscInt cellPair[2]; 316 PetscBool found = faceDepth > 1 ? PETSC_TRUE : PETSC_FALSE; 317 PetscInt meetSize = 0; 318 const PetscInt *meet = NULL; 319 320 cellPair[0] = cell; cellPair[1] = neighborCells[n]; 321 if (cellPair[0] == cellPair[1]) continue; 322 if (!found) { 323 ierr = DMPlexGetMeet(dm, 2, cellPair, &meetSize, &meet);CHKERRQ(ierr); 324 if (meetSize) { 325 PetscInt f; 326 327 for (f = 0; f < numFaceCases; ++f) { 328 if (numFaceVertices[f] == meetSize) { 329 found = PETSC_TRUE; 330 break; 331 } 332 } 333 } 334 ierr = DMPlexRestoreMeet(dm, 2, cellPair, &meetSize, &meet);CHKERRQ(ierr); 335 } 336 if (found) ++off[cell-cStart+1]; 337 } 338 } 339 /* Prefix sum */ 340 for (cell = 1; cell <= numCells; ++cell) off[cell] += off[cell-1]; 341 342 if (adjacency) { 343 ierr = PetscMalloc1(off[numCells], &adj);CHKERRQ(ierr); 344 /* Get neighboring cells */ 345 for (cell = cStart; cell < cEnd; ++cell) { 346 PetscInt numNeighbors = PETSC_DETERMINE, n; 347 PetscInt cellOffset = 0; 348 349 ierr = DMPlexGetAdjacency_Internal(dm, cell, PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, &numNeighbors, &neighborCells);CHKERRQ(ierr); 350 /* Get meet with each cell, and check with recognizer (could optimize to check each pair only once) */ 351 for (n = 0; n < numNeighbors; ++n) { 352 PetscInt cellPair[2]; 353 PetscBool found = faceDepth > 1 ? PETSC_TRUE : PETSC_FALSE; 354 PetscInt meetSize = 0; 355 const PetscInt *meet = NULL; 356 357 cellPair[0] = cell; cellPair[1] = neighborCells[n]; 358 if (cellPair[0] == cellPair[1]) continue; 359 if (!found) { 360 ierr = DMPlexGetMeet(dm, 2, cellPair, &meetSize, &meet);CHKERRQ(ierr); 361 if (meetSize) { 362 PetscInt f; 363 364 for (f = 0; f < numFaceCases; ++f) { 365 if (numFaceVertices[f] == meetSize) { 366 found = PETSC_TRUE; 367 break; 368 } 369 } 370 } 371 ierr = DMPlexRestoreMeet(dm, 2, cellPair, &meetSize, &meet);CHKERRQ(ierr); 372 } 373 if (found) { 374 adj[off[cell-cStart]+cellOffset] = neighborCells[n]; 375 ++cellOffset; 376 } 377 } 378 } 379 } 380 ierr = PetscFree(neighborCells);CHKERRQ(ierr); 381 if (numVertices) *numVertices = numCells; 382 if (offsets) *offsets = off; 383 if (adjacency) *adjacency = adj; 384 PetscFunctionReturn(0); 385 } 386 387 /*@C 388 PetscPartitionerRegister - Adds a new PetscPartitioner implementation 389 390 Not Collective 391 392 Input Parameters: 393 + name - The name of a new user-defined creation routine 394 - create_func - The creation routine itself 395 396 Notes: 397 PetscPartitionerRegister() may be called multiple times to add several user-defined PetscPartitioners 398 399 Sample usage: 400 .vb 401 PetscPartitionerRegister("my_part", MyPetscPartitionerCreate); 402 .ve 403 404 Then, your PetscPartitioner type can be chosen with the procedural interface via 405 .vb 406 PetscPartitionerCreate(MPI_Comm, PetscPartitioner *); 407 PetscPartitionerSetType(PetscPartitioner, "my_part"); 408 .ve 409 or at runtime via the option 410 .vb 411 -petscpartitioner_type my_part 412 .ve 413 414 Level: advanced 415 416 .keywords: PetscPartitioner, register 417 .seealso: PetscPartitionerRegisterAll(), PetscPartitionerRegisterDestroy() 418 419 @*/ 420 PetscErrorCode PetscPartitionerRegister(const char sname[], PetscErrorCode (*function)(PetscPartitioner)) 421 { 422 PetscErrorCode ierr; 423 424 PetscFunctionBegin; 425 ierr = PetscFunctionListAdd(&PetscPartitionerList, sname, function);CHKERRQ(ierr); 426 PetscFunctionReturn(0); 427 } 428 429 /*@C 430 PetscPartitionerSetType - Builds a particular PetscPartitioner 431 432 Collective on PetscPartitioner 433 434 Input Parameters: 435 + part - The PetscPartitioner object 436 - name - The kind of partitioner 437 438 Options Database Key: 439 . -petscpartitioner_type <type> - Sets the PetscPartitioner type; use -help for a list of available types 440 441 Level: intermediate 442 443 .keywords: PetscPartitioner, set, type 444 .seealso: PetscPartitionerGetType(), PetscPartitionerCreate() 445 @*/ 446 PetscErrorCode PetscPartitionerSetType(PetscPartitioner part, PetscPartitionerType name) 447 { 448 PetscErrorCode (*r)(PetscPartitioner); 449 PetscBool match; 450 PetscErrorCode ierr; 451 452 PetscFunctionBegin; 453 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 454 ierr = PetscObjectTypeCompare((PetscObject) part, name, &match);CHKERRQ(ierr); 455 if (match) PetscFunctionReturn(0); 456 457 ierr = PetscPartitionerRegisterAll();CHKERRQ(ierr); 458 ierr = PetscFunctionListFind(PetscPartitionerList, name, &r);CHKERRQ(ierr); 459 if (!r) SETERRQ1(PetscObjectComm((PetscObject) part), PETSC_ERR_ARG_UNKNOWN_TYPE, "Unknown PetscPartitioner type: %s", name); 460 461 if (part->ops->destroy) { 462 ierr = (*part->ops->destroy)(part);CHKERRQ(ierr); 463 } 464 ierr = PetscMemzero(part->ops, sizeof(struct _PetscPartitionerOps));CHKERRQ(ierr); 465 ierr = (*r)(part);CHKERRQ(ierr); 466 ierr = PetscObjectChangeTypeName((PetscObject) part, name);CHKERRQ(ierr); 467 PetscFunctionReturn(0); 468 } 469 470 /*@C 471 PetscPartitionerGetType - Gets the PetscPartitioner type name (as a string) from the object. 472 473 Not Collective 474 475 Input Parameter: 476 . part - The PetscPartitioner 477 478 Output Parameter: 479 . name - The PetscPartitioner type name 480 481 Level: intermediate 482 483 .keywords: PetscPartitioner, get, type, name 484 .seealso: PetscPartitionerSetType(), PetscPartitionerCreate() 485 @*/ 486 PetscErrorCode PetscPartitionerGetType(PetscPartitioner part, PetscPartitionerType *name) 487 { 488 PetscErrorCode ierr; 489 490 PetscFunctionBegin; 491 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 492 PetscValidPointer(name, 2); 493 ierr = PetscPartitionerRegisterAll();CHKERRQ(ierr); 494 *name = ((PetscObject) part)->type_name; 495 PetscFunctionReturn(0); 496 } 497 498 /*@C 499 PetscPartitionerView - Views a PetscPartitioner 500 501 Collective on PetscPartitioner 502 503 Input Parameter: 504 + part - the PetscPartitioner object to view 505 - v - the viewer 506 507 Level: developer 508 509 .seealso: PetscPartitionerDestroy() 510 @*/ 511 PetscErrorCode PetscPartitionerView(PetscPartitioner part, PetscViewer v) 512 { 513 PetscMPIInt size; 514 PetscBool isascii; 515 PetscErrorCode ierr; 516 517 PetscFunctionBegin; 518 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 519 if (!v) {ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject) part), &v);CHKERRQ(ierr);} 520 ierr = PetscObjectTypeCompare((PetscObject) v, PETSCVIEWERASCII, &isascii);CHKERRQ(ierr); 521 if (isascii) { 522 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) part), &size);CHKERRQ(ierr); 523 ierr = PetscViewerASCIIPrintf(v, "Graph Partitioner: %d MPI Process%s\n", size, size > 1 ? "es" : "");CHKERRQ(ierr); 524 ierr = PetscViewerASCIIPrintf(v, " type: %s\n", part->hdr.type_name);CHKERRQ(ierr); 525 ierr = PetscViewerASCIIPushTab(v);CHKERRQ(ierr); 526 ierr = PetscViewerASCIIPrintf(v, "edge cut: %D\n", part->edgeCut);CHKERRQ(ierr); 527 ierr = PetscViewerASCIIPrintf(v, "balance: %.2g\n", part->balance);CHKERRQ(ierr); 528 ierr = PetscViewerASCIIPopTab(v);CHKERRQ(ierr); 529 } 530 if (part->ops->view) {ierr = (*part->ops->view)(part, v);CHKERRQ(ierr);} 531 PetscFunctionReturn(0); 532 } 533 534 static PetscErrorCode PetscPartitionerGetDefaultType(const char *currentType, const char **defaultType) 535 { 536 PetscFunctionBegin; 537 if (!currentType) { 538 #if defined(PETSC_HAVE_CHACO) 539 *defaultType = PETSCPARTITIONERCHACO; 540 #elif defined(PETSC_HAVE_PARMETIS) 541 *defaultType = PETSCPARTITIONERPARMETIS; 542 #elif defined(PETSC_HAVE_PTSCOTCH) 543 *defaultType = PETSCPARTITIONERPTSCOTCH; 544 #else 545 *defaultType = PETSCPARTITIONERSIMPLE; 546 #endif 547 } else { 548 *defaultType = currentType; 549 } 550 PetscFunctionReturn(0); 551 } 552 553 /*@ 554 PetscPartitionerSetFromOptions - sets parameters in a PetscPartitioner from the options database 555 556 Collective on PetscPartitioner 557 558 Input Parameter: 559 . part - the PetscPartitioner object to set options for 560 561 Level: developer 562 563 .seealso: PetscPartitionerView() 564 @*/ 565 PetscErrorCode PetscPartitionerSetFromOptions(PetscPartitioner part) 566 { 567 const char *defaultType; 568 char name[256]; 569 PetscBool flg; 570 PetscErrorCode ierr; 571 572 PetscFunctionBegin; 573 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 574 ierr = PetscPartitionerRegisterAll();CHKERRQ(ierr); 575 ierr = PetscPartitionerGetDefaultType(((PetscObject) part)->type_name,&defaultType);CHKERRQ(ierr); 576 ierr = PetscObjectOptionsBegin((PetscObject) part);CHKERRQ(ierr); 577 ierr = PetscOptionsFList("-petscpartitioner_type", "Graph partitioner", "PetscPartitionerSetType", PetscPartitionerList, defaultType, name, sizeof(name), &flg);CHKERRQ(ierr); 578 if (flg) { 579 ierr = PetscPartitionerSetType(part, name);CHKERRQ(ierr); 580 } else if (!((PetscObject) part)->type_name) { 581 ierr = PetscPartitionerSetType(part, defaultType);CHKERRQ(ierr); 582 } 583 if (part->ops->setfromoptions) { 584 ierr = (*part->ops->setfromoptions)(PetscOptionsObject,part);CHKERRQ(ierr); 585 } 586 ierr = PetscOptionsGetViewer(((PetscObject) part)->comm, ((PetscObject) part)->options, ((PetscObject) part)->prefix, "-petscpartitioner_view_graph", &part->viewerGraph, &part->formatGraph, &part->viewGraph);CHKERRQ(ierr); 587 /* process any options handlers added with PetscObjectAddOptionsHandler() */ 588 ierr = PetscObjectProcessOptionsHandlers(PetscOptionsObject,(PetscObject) part);CHKERRQ(ierr); 589 ierr = PetscOptionsEnd();CHKERRQ(ierr); 590 PetscFunctionReturn(0); 591 } 592 593 /*@C 594 PetscPartitionerSetUp - Construct data structures for the PetscPartitioner 595 596 Collective on PetscPartitioner 597 598 Input Parameter: 599 . part - the PetscPartitioner object to setup 600 601 Level: developer 602 603 .seealso: PetscPartitionerView(), PetscPartitionerDestroy() 604 @*/ 605 PetscErrorCode PetscPartitionerSetUp(PetscPartitioner part) 606 { 607 PetscErrorCode ierr; 608 609 PetscFunctionBegin; 610 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 611 if (part->ops->setup) {ierr = (*part->ops->setup)(part);CHKERRQ(ierr);} 612 PetscFunctionReturn(0); 613 } 614 615 /*@ 616 PetscPartitionerDestroy - Destroys a PetscPartitioner object 617 618 Collective on PetscPartitioner 619 620 Input Parameter: 621 . part - the PetscPartitioner object to destroy 622 623 Level: developer 624 625 .seealso: PetscPartitionerView() 626 @*/ 627 PetscErrorCode PetscPartitionerDestroy(PetscPartitioner *part) 628 { 629 PetscErrorCode ierr; 630 631 PetscFunctionBegin; 632 if (!*part) PetscFunctionReturn(0); 633 PetscValidHeaderSpecific((*part), PETSCPARTITIONER_CLASSID, 1); 634 635 if (--((PetscObject)(*part))->refct > 0) {*part = 0; PetscFunctionReturn(0);} 636 ((PetscObject) (*part))->refct = 0; 637 638 ierr = PetscViewerDestroy(&(*part)->viewerGraph);CHKERRQ(ierr); 639 if ((*part)->ops->destroy) {ierr = (*(*part)->ops->destroy)(*part);CHKERRQ(ierr);} 640 ierr = PetscHeaderDestroy(part);CHKERRQ(ierr); 641 PetscFunctionReturn(0); 642 } 643 644 /*@ 645 PetscPartitionerCreate - Creates an empty PetscPartitioner object. The type can then be set with PetscPartitionerSetType(). 646 647 Collective on MPI_Comm 648 649 Input Parameter: 650 . comm - The communicator for the PetscPartitioner object 651 652 Output Parameter: 653 . part - The PetscPartitioner object 654 655 Level: beginner 656 657 .seealso: PetscPartitionerSetType(), PETSCPARTITIONERCHACO, PETSCPARTITIONERPARMETIS, PETSCPARTITIONERSHELL, PETSCPARTITIONERSIMPLE, PETSCPARTITIONERGATHER 658 @*/ 659 PetscErrorCode PetscPartitionerCreate(MPI_Comm comm, PetscPartitioner *part) 660 { 661 PetscPartitioner p; 662 const char *partitionerType = NULL; 663 PetscErrorCode ierr; 664 665 PetscFunctionBegin; 666 PetscValidPointer(part, 2); 667 *part = NULL; 668 ierr = DMInitializePackage();CHKERRQ(ierr); 669 670 ierr = PetscHeaderCreate(p, PETSCPARTITIONER_CLASSID, "PetscPartitioner", "Graph Partitioner", "PetscPartitioner", comm, PetscPartitionerDestroy, PetscPartitionerView);CHKERRQ(ierr); 671 ierr = PetscPartitionerGetDefaultType(NULL,&partitionerType);CHKERRQ(ierr); 672 ierr = PetscPartitionerSetType(p,partitionerType);CHKERRQ(ierr); 673 674 p->edgeCut = 0; 675 p->balance = 0.0; 676 677 *part = p; 678 PetscFunctionReturn(0); 679 } 680 681 /*@ 682 PetscPartitionerPartition - Create a non-overlapping partition of the cells in the mesh 683 684 Collective on DM 685 686 Input Parameters: 687 + part - The PetscPartitioner 688 - dm - The mesh DM 689 690 Output Parameters: 691 + partSection - The PetscSection giving the division of points by partition 692 - partition - The list of points by partition 693 694 Options Database: 695 . -petscpartitioner_view_graph - View the graph we are partitioning 696 697 Note: Instead of cells, points at a given height can be partitioned by calling PetscPartitionerSetPointHeight() 698 699 Level: developer 700 701 .seealso DMPlexDistribute(), PetscPartitionerSetPointHeight(), PetscPartitionerCreate() 702 @*/ 703 PetscErrorCode PetscPartitionerPartition(PetscPartitioner part, DM dm, PetscSection partSection, IS *partition) 704 { 705 PetscMPIInt size; 706 PetscErrorCode ierr; 707 708 PetscFunctionBegin; 709 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 710 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 711 PetscValidHeaderSpecific(partSection, PETSC_SECTION_CLASSID, 4); 712 PetscValidPointer(partition, 5); 713 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) part), &size);CHKERRQ(ierr); 714 if (size == 1) { 715 PetscInt *points; 716 PetscInt cStart, cEnd, c; 717 718 ierr = DMPlexGetHeightStratum(dm, part->height, &cStart, &cEnd);CHKERRQ(ierr); 719 ierr = PetscSectionSetChart(partSection, 0, size);CHKERRQ(ierr); 720 ierr = PetscSectionSetDof(partSection, 0, cEnd-cStart);CHKERRQ(ierr); 721 ierr = PetscSectionSetUp(partSection);CHKERRQ(ierr); 722 ierr = PetscMalloc1(cEnd-cStart, &points);CHKERRQ(ierr); 723 for (c = cStart; c < cEnd; ++c) points[c] = c; 724 ierr = ISCreateGeneral(PetscObjectComm((PetscObject) part), cEnd-cStart, points, PETSC_OWN_POINTER, partition);CHKERRQ(ierr); 725 PetscFunctionReturn(0); 726 } 727 if (part->height == 0) { 728 PetscInt numVertices; 729 PetscInt *start = NULL; 730 PetscInt *adjacency = NULL; 731 IS globalNumbering; 732 733 ierr = DMPlexCreatePartitionerGraph(dm, 0, &numVertices, &start, &adjacency, &globalNumbering);CHKERRQ(ierr); 734 if (part->viewGraph) { 735 PetscViewer viewer = part->viewerGraph; 736 PetscBool isascii; 737 PetscInt v, i; 738 PetscMPIInt rank; 739 740 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) viewer), &rank);CHKERRQ(ierr); 741 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &isascii);CHKERRQ(ierr); 742 if (isascii) { 743 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 744 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%d]Nv: %D\n", rank, numVertices);CHKERRQ(ierr); 745 for (v = 0; v < numVertices; ++v) { 746 const PetscInt s = start[v]; 747 const PetscInt e = start[v+1]; 748 749 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%d] ", rank);CHKERRQ(ierr); 750 for (i = s; i < e; ++i) {ierr = PetscViewerASCIISynchronizedPrintf(viewer, "%D ", adjacency[i]);CHKERRQ(ierr);} 751 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%D-%D)\n", s, e);CHKERRQ(ierr); 752 } 753 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 754 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 755 } 756 } 757 if (!part->ops->partition) SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_ARG_WRONGSTATE, "PetscPartitioner has no type"); 758 ierr = (*part->ops->partition)(part, dm, size, numVertices, start, adjacency, partSection, partition);CHKERRQ(ierr); 759 ierr = PetscFree(start);CHKERRQ(ierr); 760 ierr = PetscFree(adjacency);CHKERRQ(ierr); 761 if (globalNumbering) { /* partition is wrt global unique numbering: change this to be wrt local numbering */ 762 const PetscInt *globalNum; 763 const PetscInt *partIdx; 764 PetscInt *map, cStart, cEnd; 765 PetscInt *adjusted, i, localSize, offset; 766 IS newPartition; 767 768 ierr = ISGetLocalSize(*partition,&localSize);CHKERRQ(ierr); 769 ierr = PetscMalloc1(localSize,&adjusted);CHKERRQ(ierr); 770 ierr = ISGetIndices(globalNumbering,&globalNum);CHKERRQ(ierr); 771 ierr = ISGetIndices(*partition,&partIdx);CHKERRQ(ierr); 772 ierr = PetscMalloc1(localSize,&map);CHKERRQ(ierr); 773 ierr = DMPlexGetHeightStratum(dm, part->height, &cStart, &cEnd);CHKERRQ(ierr); 774 for (i = cStart, offset = 0; i < cEnd; i++) { 775 if (globalNum[i - cStart] >= 0) map[offset++] = i; 776 } 777 for (i = 0; i < localSize; i++) { 778 adjusted[i] = map[partIdx[i]]; 779 } 780 ierr = PetscFree(map);CHKERRQ(ierr); 781 ierr = ISRestoreIndices(*partition,&partIdx);CHKERRQ(ierr); 782 ierr = ISRestoreIndices(globalNumbering,&globalNum);CHKERRQ(ierr); 783 ierr = ISCreateGeneral(PETSC_COMM_SELF,localSize,adjusted,PETSC_OWN_POINTER,&newPartition);CHKERRQ(ierr); 784 ierr = ISDestroy(&globalNumbering);CHKERRQ(ierr); 785 ierr = ISDestroy(partition);CHKERRQ(ierr); 786 *partition = newPartition; 787 } 788 } else SETERRQ1(PetscObjectComm((PetscObject) part), PETSC_ERR_ARG_OUTOFRANGE, "Invalid height %D for points to partition", part->height); 789 ierr = PetscPartitionerViewFromOptions(part, NULL, "-petscpartitioner_view");CHKERRQ(ierr); 790 PetscFunctionReturn(0); 791 } 792 793 static PetscErrorCode PetscPartitionerDestroy_Shell(PetscPartitioner part) 794 { 795 PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data; 796 PetscErrorCode ierr; 797 798 PetscFunctionBegin; 799 ierr = PetscSectionDestroy(&p->section);CHKERRQ(ierr); 800 ierr = ISDestroy(&p->partition);CHKERRQ(ierr); 801 ierr = PetscFree(p);CHKERRQ(ierr); 802 PetscFunctionReturn(0); 803 } 804 805 static PetscErrorCode PetscPartitionerView_Shell_Ascii(PetscPartitioner part, PetscViewer viewer) 806 { 807 PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data; 808 PetscErrorCode ierr; 809 810 PetscFunctionBegin; 811 if (p->random) { 812 ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); 813 ierr = PetscViewerASCIIPrintf(viewer, "using random partition\n");CHKERRQ(ierr); 814 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 815 } 816 PetscFunctionReturn(0); 817 } 818 819 static PetscErrorCode PetscPartitionerView_Shell(PetscPartitioner part, PetscViewer viewer) 820 { 821 PetscBool iascii; 822 PetscErrorCode ierr; 823 824 PetscFunctionBegin; 825 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 826 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 827 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);CHKERRQ(ierr); 828 if (iascii) {ierr = PetscPartitionerView_Shell_Ascii(part, viewer);CHKERRQ(ierr);} 829 PetscFunctionReturn(0); 830 } 831 832 static PetscErrorCode PetscPartitionerSetFromOptions_Shell(PetscOptionItems *PetscOptionsObject, PetscPartitioner part) 833 { 834 PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data; 835 PetscErrorCode ierr; 836 837 PetscFunctionBegin; 838 ierr = PetscOptionsHead(PetscOptionsObject, "PetscPartitioner Shell Options");CHKERRQ(ierr); 839 ierr = PetscOptionsBool("-petscpartitioner_shell_random", "Use a random partition", "PetscPartitionerView", PETSC_FALSE, &p->random, NULL);CHKERRQ(ierr); 840 ierr = PetscOptionsTail();CHKERRQ(ierr); 841 PetscFunctionReturn(0); 842 } 843 844 static PetscErrorCode PetscPartitionerPartition_Shell(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition) 845 { 846 PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data; 847 PetscInt np; 848 PetscErrorCode ierr; 849 850 PetscFunctionBegin; 851 if (p->random) { 852 PetscRandom r; 853 PetscInt *sizes, *points, v, p; 854 PetscMPIInt rank; 855 856 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 857 ierr = PetscRandomCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 858 ierr = PetscRandomSetInterval(r, 0.0, (PetscScalar) nparts);CHKERRQ(ierr); 859 ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr); 860 ierr = PetscCalloc2(nparts, &sizes, numVertices, &points);CHKERRQ(ierr); 861 for (v = 0; v < numVertices; ++v) {points[v] = v;} 862 for (p = 0; p < nparts; ++p) {sizes[p] = numVertices/nparts + (PetscInt) (p < numVertices % nparts);} 863 for (v = numVertices-1; v > 0; --v) { 864 PetscReal val; 865 PetscInt w, tmp; 866 867 ierr = PetscRandomSetInterval(r, 0.0, (PetscScalar) (v+1));CHKERRQ(ierr); 868 ierr = PetscRandomGetValueReal(r, &val);CHKERRQ(ierr); 869 w = PetscFloorReal(val); 870 tmp = points[v]; 871 points[v] = points[w]; 872 points[w] = tmp; 873 } 874 ierr = PetscRandomDestroy(&r);CHKERRQ(ierr); 875 ierr = PetscPartitionerShellSetPartition(part, nparts, sizes, points);CHKERRQ(ierr); 876 ierr = PetscFree2(sizes, points);CHKERRQ(ierr); 877 } 878 if (!p->section) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Shell partitioner information not provided. Please call PetscPartitionerShellSetPartition()"); 879 ierr = PetscSectionGetChart(p->section, NULL, &np);CHKERRQ(ierr); 880 if (nparts != np) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of requested partitions %d != configured partitions %d", nparts, np); 881 ierr = ISGetLocalSize(p->partition, &np);CHKERRQ(ierr); 882 if (numVertices != np) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of input vertices %d != configured vertices %d", numVertices, np); 883 ierr = PetscSectionCopy(p->section, partSection);CHKERRQ(ierr); 884 *partition = p->partition; 885 ierr = PetscObjectReference((PetscObject) p->partition);CHKERRQ(ierr); 886 PetscFunctionReturn(0); 887 } 888 889 static PetscErrorCode PetscPartitionerInitialize_Shell(PetscPartitioner part) 890 { 891 PetscFunctionBegin; 892 part->ops->view = PetscPartitionerView_Shell; 893 part->ops->setfromoptions = PetscPartitionerSetFromOptions_Shell; 894 part->ops->destroy = PetscPartitionerDestroy_Shell; 895 part->ops->partition = PetscPartitionerPartition_Shell; 896 PetscFunctionReturn(0); 897 } 898 899 /*MC 900 PETSCPARTITIONERSHELL = "shell" - A PetscPartitioner object 901 902 Level: intermediate 903 904 .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType() 905 M*/ 906 907 PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_Shell(PetscPartitioner part) 908 { 909 PetscPartitioner_Shell *p; 910 PetscErrorCode ierr; 911 912 PetscFunctionBegin; 913 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 914 ierr = PetscNewLog(part, &p);CHKERRQ(ierr); 915 part->data = p; 916 917 ierr = PetscPartitionerInitialize_Shell(part);CHKERRQ(ierr); 918 p->random = PETSC_FALSE; 919 PetscFunctionReturn(0); 920 } 921 922 /*@C 923 PetscPartitionerShellSetPartition - Set an artifical partition for a mesh 924 925 Collective on Part 926 927 Input Parameters: 928 + part - The PetscPartitioner 929 . size - The number of partitions 930 . sizes - array of size size (or NULL) providing the number of points in each partition 931 - points - array of size sum(sizes) (may be NULL iff sizes is NULL), a permutation of the points that groups those assigned to each partition in order (i.e., partition 0 first, partition 1 next, etc.) 932 933 Level: developer 934 935 Notes: 936 937 It is safe to free the sizes and points arrays after use in this routine. 938 939 .seealso DMPlexDistribute(), PetscPartitionerCreate() 940 @*/ 941 PetscErrorCode PetscPartitionerShellSetPartition(PetscPartitioner part, PetscInt size, const PetscInt sizes[], const PetscInt points[]) 942 { 943 PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data; 944 PetscInt proc, numPoints; 945 PetscErrorCode ierr; 946 947 PetscFunctionBegin; 948 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 949 if (sizes) {PetscValidPointer(sizes, 3);} 950 if (points) {PetscValidPointer(points, 4);} 951 ierr = PetscSectionDestroy(&p->section);CHKERRQ(ierr); 952 ierr = ISDestroy(&p->partition);CHKERRQ(ierr); 953 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) part), &p->section);CHKERRQ(ierr); 954 ierr = PetscSectionSetChart(p->section, 0, size);CHKERRQ(ierr); 955 if (sizes) { 956 for (proc = 0; proc < size; ++proc) { 957 ierr = PetscSectionSetDof(p->section, proc, sizes[proc]);CHKERRQ(ierr); 958 } 959 } 960 ierr = PetscSectionSetUp(p->section);CHKERRQ(ierr); 961 ierr = PetscSectionGetStorageSize(p->section, &numPoints);CHKERRQ(ierr); 962 ierr = ISCreateGeneral(PetscObjectComm((PetscObject) part), numPoints, points, PETSC_COPY_VALUES, &p->partition);CHKERRQ(ierr); 963 PetscFunctionReturn(0); 964 } 965 966 /*@ 967 PetscPartitionerShellSetRandom - Set the flag to use a random partition 968 969 Collective on Part 970 971 Input Parameters: 972 + part - The PetscPartitioner 973 - random - The flag to use a random partition 974 975 Level: intermediate 976 977 .seealso PetscPartitionerShellGetRandom(), PetscPartitionerCreate() 978 @*/ 979 PetscErrorCode PetscPartitionerShellSetRandom(PetscPartitioner part, PetscBool random) 980 { 981 PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data; 982 983 PetscFunctionBegin; 984 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 985 p->random = random; 986 PetscFunctionReturn(0); 987 } 988 989 /*@ 990 PetscPartitionerShellGetRandom - get the flag to use a random partition 991 992 Collective on Part 993 994 Input Parameter: 995 . part - The PetscPartitioner 996 997 Output Parameter 998 . random - The flag to use a random partition 999 1000 Level: intermediate 1001 1002 .seealso PetscPartitionerShellSetRandom(), PetscPartitionerCreate() 1003 @*/ 1004 PetscErrorCode PetscPartitionerShellGetRandom(PetscPartitioner part, PetscBool *random) 1005 { 1006 PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data; 1007 1008 PetscFunctionBegin; 1009 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 1010 PetscValidPointer(random, 2); 1011 *random = p->random; 1012 PetscFunctionReturn(0); 1013 } 1014 1015 static PetscErrorCode PetscPartitionerDestroy_Simple(PetscPartitioner part) 1016 { 1017 PetscPartitioner_Simple *p = (PetscPartitioner_Simple *) part->data; 1018 PetscErrorCode ierr; 1019 1020 PetscFunctionBegin; 1021 ierr = PetscFree(p);CHKERRQ(ierr); 1022 PetscFunctionReturn(0); 1023 } 1024 1025 static PetscErrorCode PetscPartitionerView_Simple_Ascii(PetscPartitioner part, PetscViewer viewer) 1026 { 1027 PetscFunctionBegin; 1028 PetscFunctionReturn(0); 1029 } 1030 1031 static PetscErrorCode PetscPartitionerView_Simple(PetscPartitioner part, PetscViewer viewer) 1032 { 1033 PetscBool iascii; 1034 PetscErrorCode ierr; 1035 1036 PetscFunctionBegin; 1037 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 1038 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 1039 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);CHKERRQ(ierr); 1040 if (iascii) {ierr = PetscPartitionerView_Simple_Ascii(part, viewer);CHKERRQ(ierr);} 1041 PetscFunctionReturn(0); 1042 } 1043 1044 static PetscErrorCode PetscPartitionerPartition_Simple(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition) 1045 { 1046 MPI_Comm comm; 1047 PetscInt np; 1048 PetscMPIInt size; 1049 PetscErrorCode ierr; 1050 1051 PetscFunctionBegin; 1052 comm = PetscObjectComm((PetscObject)dm); 1053 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1054 ierr = PetscSectionSetChart(partSection, 0, nparts);CHKERRQ(ierr); 1055 ierr = ISCreateStride(PETSC_COMM_SELF, numVertices, 0, 1, partition);CHKERRQ(ierr); 1056 if (size == 1) { 1057 for (np = 0; np < nparts; ++np) {ierr = PetscSectionSetDof(partSection, np, numVertices/nparts + ((numVertices % nparts) > np));CHKERRQ(ierr);} 1058 } 1059 else { 1060 PetscMPIInt rank; 1061 PetscInt nvGlobal, *offsets, myFirst, myLast; 1062 1063 ierr = PetscMalloc1(size+1,&offsets);CHKERRQ(ierr); 1064 offsets[0] = 0; 1065 ierr = MPI_Allgather(&numVertices,1,MPIU_INT,&offsets[1],1,MPIU_INT,comm);CHKERRQ(ierr); 1066 for (np = 2; np <= size; np++) { 1067 offsets[np] += offsets[np-1]; 1068 } 1069 nvGlobal = offsets[size]; 1070 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1071 myFirst = offsets[rank]; 1072 myLast = offsets[rank + 1] - 1; 1073 ierr = PetscFree(offsets);CHKERRQ(ierr); 1074 if (numVertices) { 1075 PetscInt firstPart = 0, firstLargePart = 0; 1076 PetscInt lastPart = 0, lastLargePart = 0; 1077 PetscInt rem = nvGlobal % nparts; 1078 PetscInt pSmall = nvGlobal/nparts; 1079 PetscInt pBig = nvGlobal/nparts + 1; 1080 1081 1082 if (rem) { 1083 firstLargePart = myFirst / pBig; 1084 lastLargePart = myLast / pBig; 1085 1086 if (firstLargePart < rem) { 1087 firstPart = firstLargePart; 1088 } 1089 else { 1090 firstPart = rem + (myFirst - (rem * pBig)) / pSmall; 1091 } 1092 if (lastLargePart < rem) { 1093 lastPart = lastLargePart; 1094 } 1095 else { 1096 lastPart = rem + (myLast - (rem * pBig)) / pSmall; 1097 } 1098 } 1099 else { 1100 firstPart = myFirst / (nvGlobal/nparts); 1101 lastPart = myLast / (nvGlobal/nparts); 1102 } 1103 1104 for (np = firstPart; np <= lastPart; np++) { 1105 PetscInt PartStart = np * (nvGlobal/nparts) + PetscMin(nvGlobal % nparts,np); 1106 PetscInt PartEnd = (np+1) * (nvGlobal/nparts) + PetscMin(nvGlobal % nparts,np+1); 1107 1108 PartStart = PetscMax(PartStart,myFirst); 1109 PartEnd = PetscMin(PartEnd,myLast+1); 1110 ierr = PetscSectionSetDof(partSection,np,PartEnd-PartStart);CHKERRQ(ierr); 1111 } 1112 } 1113 } 1114 ierr = PetscSectionSetUp(partSection);CHKERRQ(ierr); 1115 PetscFunctionReturn(0); 1116 } 1117 1118 static PetscErrorCode PetscPartitionerInitialize_Simple(PetscPartitioner part) 1119 { 1120 PetscFunctionBegin; 1121 part->ops->view = PetscPartitionerView_Simple; 1122 part->ops->destroy = PetscPartitionerDestroy_Simple; 1123 part->ops->partition = PetscPartitionerPartition_Simple; 1124 PetscFunctionReturn(0); 1125 } 1126 1127 /*MC 1128 PETSCPARTITIONERSIMPLE = "simple" - A PetscPartitioner object 1129 1130 Level: intermediate 1131 1132 .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType() 1133 M*/ 1134 1135 PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_Simple(PetscPartitioner part) 1136 { 1137 PetscPartitioner_Simple *p; 1138 PetscErrorCode ierr; 1139 1140 PetscFunctionBegin; 1141 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 1142 ierr = PetscNewLog(part, &p);CHKERRQ(ierr); 1143 part->data = p; 1144 1145 ierr = PetscPartitionerInitialize_Simple(part);CHKERRQ(ierr); 1146 PetscFunctionReturn(0); 1147 } 1148 1149 static PetscErrorCode PetscPartitionerDestroy_Gather(PetscPartitioner part) 1150 { 1151 PetscPartitioner_Gather *p = (PetscPartitioner_Gather *) part->data; 1152 PetscErrorCode ierr; 1153 1154 PetscFunctionBegin; 1155 ierr = PetscFree(p);CHKERRQ(ierr); 1156 PetscFunctionReturn(0); 1157 } 1158 1159 static PetscErrorCode PetscPartitionerView_Gather_Ascii(PetscPartitioner part, PetscViewer viewer) 1160 { 1161 PetscFunctionBegin; 1162 PetscFunctionReturn(0); 1163 } 1164 1165 static PetscErrorCode PetscPartitionerView_Gather(PetscPartitioner part, PetscViewer viewer) 1166 { 1167 PetscBool iascii; 1168 PetscErrorCode ierr; 1169 1170 PetscFunctionBegin; 1171 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 1172 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 1173 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);CHKERRQ(ierr); 1174 if (iascii) {ierr = PetscPartitionerView_Gather_Ascii(part, viewer);CHKERRQ(ierr);} 1175 PetscFunctionReturn(0); 1176 } 1177 1178 static PetscErrorCode PetscPartitionerPartition_Gather(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition) 1179 { 1180 PetscInt np; 1181 PetscErrorCode ierr; 1182 1183 PetscFunctionBegin; 1184 ierr = PetscSectionSetChart(partSection, 0, nparts);CHKERRQ(ierr); 1185 ierr = ISCreateStride(PETSC_COMM_SELF, numVertices, 0, 1, partition);CHKERRQ(ierr); 1186 ierr = PetscSectionSetDof(partSection,0,numVertices);CHKERRQ(ierr); 1187 for (np = 1; np < nparts; ++np) {ierr = PetscSectionSetDof(partSection, np, 0);CHKERRQ(ierr);} 1188 ierr = PetscSectionSetUp(partSection);CHKERRQ(ierr); 1189 PetscFunctionReturn(0); 1190 } 1191 1192 static PetscErrorCode PetscPartitionerInitialize_Gather(PetscPartitioner part) 1193 { 1194 PetscFunctionBegin; 1195 part->ops->view = PetscPartitionerView_Gather; 1196 part->ops->destroy = PetscPartitionerDestroy_Gather; 1197 part->ops->partition = PetscPartitionerPartition_Gather; 1198 PetscFunctionReturn(0); 1199 } 1200 1201 /*MC 1202 PETSCPARTITIONERGATHER = "gather" - A PetscPartitioner object 1203 1204 Level: intermediate 1205 1206 .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType() 1207 M*/ 1208 1209 PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_Gather(PetscPartitioner part) 1210 { 1211 PetscPartitioner_Gather *p; 1212 PetscErrorCode ierr; 1213 1214 PetscFunctionBegin; 1215 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 1216 ierr = PetscNewLog(part, &p);CHKERRQ(ierr); 1217 part->data = p; 1218 1219 ierr = PetscPartitionerInitialize_Gather(part);CHKERRQ(ierr); 1220 PetscFunctionReturn(0); 1221 } 1222 1223 1224 static PetscErrorCode PetscPartitionerDestroy_Chaco(PetscPartitioner part) 1225 { 1226 PetscPartitioner_Chaco *p = (PetscPartitioner_Chaco *) part->data; 1227 PetscErrorCode ierr; 1228 1229 PetscFunctionBegin; 1230 ierr = PetscFree(p);CHKERRQ(ierr); 1231 PetscFunctionReturn(0); 1232 } 1233 1234 static PetscErrorCode PetscPartitionerView_Chaco_Ascii(PetscPartitioner part, PetscViewer viewer) 1235 { 1236 PetscFunctionBegin; 1237 PetscFunctionReturn(0); 1238 } 1239 1240 static PetscErrorCode PetscPartitionerView_Chaco(PetscPartitioner part, PetscViewer viewer) 1241 { 1242 PetscBool iascii; 1243 PetscErrorCode ierr; 1244 1245 PetscFunctionBegin; 1246 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 1247 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 1248 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);CHKERRQ(ierr); 1249 if (iascii) {ierr = PetscPartitionerView_Chaco_Ascii(part, viewer);CHKERRQ(ierr);} 1250 PetscFunctionReturn(0); 1251 } 1252 1253 #if defined(PETSC_HAVE_CHACO) 1254 #if defined(PETSC_HAVE_UNISTD_H) 1255 #include <unistd.h> 1256 #endif 1257 #if defined(PETSC_HAVE_CHACO_INT_ASSIGNMENT) 1258 #include <chaco.h> 1259 #else 1260 /* Older versions of Chaco do not have an include file */ 1261 PETSC_EXTERN int interface(int nvtxs, int *start, int *adjacency, int *vwgts, 1262 float *ewgts, float *x, float *y, float *z, char *outassignname, 1263 char *outfilename, short *assignment, int architecture, int ndims_tot, 1264 int mesh_dims[3], double *goal, int global_method, int local_method, 1265 int rqi_flag, int vmax, int ndims, double eigtol, long seed); 1266 #endif 1267 extern int FREE_GRAPH; 1268 #endif 1269 1270 static PetscErrorCode PetscPartitionerPartition_Chaco(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition) 1271 { 1272 #if defined(PETSC_HAVE_CHACO) 1273 enum {DEFAULT_METHOD = 1, INERTIAL_METHOD = 3}; 1274 MPI_Comm comm; 1275 int nvtxs = numVertices; /* number of vertices in full graph */ 1276 int *vwgts = NULL; /* weights for all vertices */ 1277 float *ewgts = NULL; /* weights for all edges */ 1278 float *x = NULL, *y = NULL, *z = NULL; /* coordinates for inertial method */ 1279 char *outassignname = NULL; /* name of assignment output file */ 1280 char *outfilename = NULL; /* output file name */ 1281 int architecture = 1; /* 0 => hypercube, d => d-dimensional mesh */ 1282 int ndims_tot = 0; /* total number of cube dimensions to divide */ 1283 int mesh_dims[3]; /* dimensions of mesh of processors */ 1284 double *goal = NULL; /* desired set sizes for each set */ 1285 int global_method = 1; /* global partitioning algorithm */ 1286 int local_method = 1; /* local partitioning algorithm */ 1287 int rqi_flag = 0; /* should I use RQI/Symmlq eigensolver? */ 1288 int vmax = 200; /* how many vertices to coarsen down to? */ 1289 int ndims = 1; /* number of eigenvectors (2^d sets) */ 1290 double eigtol = 0.001; /* tolerance on eigenvectors */ 1291 long seed = 123636512; /* for random graph mutations */ 1292 #if defined(PETSC_HAVE_CHACO_INT_ASSIGNMENT) 1293 int *assignment; /* Output partition */ 1294 #else 1295 short int *assignment; /* Output partition */ 1296 #endif 1297 int fd_stdout, fd_pipe[2]; 1298 PetscInt *points; 1299 int i, v, p; 1300 PetscErrorCode ierr; 1301 1302 PetscFunctionBegin; 1303 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1304 #if defined (PETSC_USE_DEBUG) 1305 { 1306 int ival,isum; 1307 PetscBool distributed; 1308 1309 ival = (numVertices > 0); 1310 ierr = MPI_Allreduce(&ival, &isum, 1, MPI_INT, MPI_SUM, comm);CHKERRQ(ierr); 1311 distributed = (isum > 1) ? PETSC_TRUE : PETSC_FALSE; 1312 if (distributed) SETERRQ(comm, PETSC_ERR_SUP, "Chaco cannot partition a distributed graph"); 1313 } 1314 #endif 1315 if (!numVertices) { 1316 ierr = PetscSectionSetChart(partSection, 0, nparts);CHKERRQ(ierr); 1317 ierr = PetscSectionSetUp(partSection);CHKERRQ(ierr); 1318 ierr = ISCreateGeneral(comm, 0, NULL, PETSC_OWN_POINTER, partition);CHKERRQ(ierr); 1319 PetscFunctionReturn(0); 1320 } 1321 FREE_GRAPH = 0; /* Do not let Chaco free my memory */ 1322 for (i = 0; i < start[numVertices]; ++i) ++adjacency[i]; 1323 1324 if (global_method == INERTIAL_METHOD) { 1325 /* manager.createCellCoordinates(nvtxs, &x, &y, &z); */ 1326 SETERRQ(comm, PETSC_ERR_SUP, "Inertial partitioning not yet supported"); 1327 } 1328 mesh_dims[0] = nparts; 1329 mesh_dims[1] = 1; 1330 mesh_dims[2] = 1; 1331 ierr = PetscMalloc1(nvtxs, &assignment);CHKERRQ(ierr); 1332 /* Chaco outputs to stdout. We redirect this to a buffer. */ 1333 /* TODO: check error codes for UNIX calls */ 1334 #if defined(PETSC_HAVE_UNISTD_H) 1335 { 1336 int piperet; 1337 piperet = pipe(fd_pipe); 1338 if (piperet) SETERRQ(comm,PETSC_ERR_SYS,"Could not create pipe"); 1339 fd_stdout = dup(1); 1340 close(1); 1341 dup2(fd_pipe[1], 1); 1342 } 1343 #endif 1344 ierr = interface(nvtxs, (int*) start, (int*) adjacency, vwgts, ewgts, x, y, z, outassignname, outfilename, 1345 assignment, architecture, ndims_tot, mesh_dims, goal, global_method, local_method, rqi_flag, 1346 vmax, ndims, eigtol, seed); 1347 #if defined(PETSC_HAVE_UNISTD_H) 1348 { 1349 char msgLog[10000]; 1350 int count; 1351 1352 fflush(stdout); 1353 count = read(fd_pipe[0], msgLog, (10000-1)*sizeof(char)); 1354 if (count < 0) count = 0; 1355 msgLog[count] = 0; 1356 close(1); 1357 dup2(fd_stdout, 1); 1358 close(fd_stdout); 1359 close(fd_pipe[0]); 1360 close(fd_pipe[1]); 1361 if (ierr) SETERRQ1(comm, PETSC_ERR_LIB, "Error in Chaco library: %s", msgLog); 1362 } 1363 #else 1364 if (ierr) SETERRQ1(comm, PETSC_ERR_LIB, "Error in Chaco library: %s", "error in stdout"); 1365 #endif 1366 /* Convert to PetscSection+IS */ 1367 ierr = PetscSectionSetChart(partSection, 0, nparts);CHKERRQ(ierr); 1368 for (v = 0; v < nvtxs; ++v) { 1369 ierr = PetscSectionAddDof(partSection, assignment[v], 1);CHKERRQ(ierr); 1370 } 1371 ierr = PetscSectionSetUp(partSection);CHKERRQ(ierr); 1372 ierr = PetscMalloc1(nvtxs, &points);CHKERRQ(ierr); 1373 for (p = 0, i = 0; p < nparts; ++p) { 1374 for (v = 0; v < nvtxs; ++v) { 1375 if (assignment[v] == p) points[i++] = v; 1376 } 1377 } 1378 if (i != nvtxs) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of points %D should be %D", i, nvtxs); 1379 ierr = ISCreateGeneral(comm, nvtxs, points, PETSC_OWN_POINTER, partition);CHKERRQ(ierr); 1380 if (global_method == INERTIAL_METHOD) { 1381 /* manager.destroyCellCoordinates(nvtxs, &x, &y, &z); */ 1382 } 1383 ierr = PetscFree(assignment);CHKERRQ(ierr); 1384 for (i = 0; i < start[numVertices]; ++i) --adjacency[i]; 1385 PetscFunctionReturn(0); 1386 #else 1387 SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_SUP, "Mesh partitioning needs external package support.\nPlease reconfigure with --download-chaco."); 1388 #endif 1389 } 1390 1391 static PetscErrorCode PetscPartitionerInitialize_Chaco(PetscPartitioner part) 1392 { 1393 PetscFunctionBegin; 1394 part->ops->view = PetscPartitionerView_Chaco; 1395 part->ops->destroy = PetscPartitionerDestroy_Chaco; 1396 part->ops->partition = PetscPartitionerPartition_Chaco; 1397 PetscFunctionReturn(0); 1398 } 1399 1400 /*MC 1401 PETSCPARTITIONERCHACO = "chaco" - A PetscPartitioner object using the Chaco library 1402 1403 Level: intermediate 1404 1405 .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType() 1406 M*/ 1407 1408 PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_Chaco(PetscPartitioner part) 1409 { 1410 PetscPartitioner_Chaco *p; 1411 PetscErrorCode ierr; 1412 1413 PetscFunctionBegin; 1414 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 1415 ierr = PetscNewLog(part, &p);CHKERRQ(ierr); 1416 part->data = p; 1417 1418 ierr = PetscPartitionerInitialize_Chaco(part);CHKERRQ(ierr); 1419 ierr = PetscCitationsRegister(ChacoPartitionerCitation, &ChacoPartitionercite);CHKERRQ(ierr); 1420 PetscFunctionReturn(0); 1421 } 1422 1423 static const char *ptypes[] = {"kway", "rb"}; 1424 1425 static PetscErrorCode PetscPartitionerDestroy_ParMetis(PetscPartitioner part) 1426 { 1427 PetscPartitioner_ParMetis *p = (PetscPartitioner_ParMetis *) part->data; 1428 PetscErrorCode ierr; 1429 1430 PetscFunctionBegin; 1431 ierr = PetscFree(p);CHKERRQ(ierr); 1432 PetscFunctionReturn(0); 1433 } 1434 1435 static PetscErrorCode PetscPartitionerView_ParMetis_Ascii(PetscPartitioner part, PetscViewer viewer) 1436 { 1437 PetscPartitioner_ParMetis *p = (PetscPartitioner_ParMetis *) part->data; 1438 PetscErrorCode ierr; 1439 1440 PetscFunctionBegin; 1441 ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); 1442 ierr = PetscViewerASCIIPrintf(viewer, "ParMetis type: %s\n", ptypes[p->ptype]);CHKERRQ(ierr); 1443 ierr = PetscViewerASCIIPrintf(viewer, "load imbalance ratio %g\n", (double) p->imbalanceRatio);CHKERRQ(ierr); 1444 ierr = PetscViewerASCIIPrintf(viewer, "debug flag %D\n", p->debugFlag);CHKERRQ(ierr); 1445 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 1446 PetscFunctionReturn(0); 1447 } 1448 1449 static PetscErrorCode PetscPartitionerView_ParMetis(PetscPartitioner part, PetscViewer viewer) 1450 { 1451 PetscBool iascii; 1452 PetscErrorCode ierr; 1453 1454 PetscFunctionBegin; 1455 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 1456 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 1457 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);CHKERRQ(ierr); 1458 if (iascii) {ierr = PetscPartitionerView_ParMetis_Ascii(part, viewer);CHKERRQ(ierr);} 1459 PetscFunctionReturn(0); 1460 } 1461 1462 static PetscErrorCode PetscPartitionerSetFromOptions_ParMetis(PetscOptionItems *PetscOptionsObject, PetscPartitioner part) 1463 { 1464 PetscPartitioner_ParMetis *p = (PetscPartitioner_ParMetis *) part->data; 1465 PetscErrorCode ierr; 1466 1467 PetscFunctionBegin; 1468 ierr = PetscOptionsHead(PetscOptionsObject, "PetscPartitioner ParMetis Options");CHKERRQ(ierr); 1469 ierr = PetscOptionsEList("-petscpartitioner_parmetis_type", "Partitioning method", "", ptypes, 2, ptypes[p->ptype], &p->ptype, NULL);CHKERRQ(ierr); 1470 ierr = PetscOptionsReal("-petscpartitioner_parmetis_imbalance_ratio", "Load imbalance ratio limit", "", p->imbalanceRatio, &p->imbalanceRatio, NULL);CHKERRQ(ierr); 1471 ierr = PetscOptionsInt("-petscpartitioner_parmetis_debug", "Debugging flag", "", p->debugFlag, &p->debugFlag, NULL);CHKERRQ(ierr); 1472 ierr = PetscOptionsTail();CHKERRQ(ierr); 1473 PetscFunctionReturn(0); 1474 } 1475 1476 #if defined(PETSC_HAVE_PARMETIS) 1477 #include <parmetis.h> 1478 #endif 1479 1480 static PetscErrorCode PetscPartitionerPartition_ParMetis(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition) 1481 { 1482 #if defined(PETSC_HAVE_PARMETIS) 1483 PetscPartitioner_ParMetis *pm = (PetscPartitioner_ParMetis *) part->data; 1484 MPI_Comm comm; 1485 PetscSection section; 1486 PetscInt nvtxs = numVertices; /* The number of vertices in full graph */ 1487 PetscInt *vtxdist; /* Distribution of vertices across processes */ 1488 PetscInt *xadj = start; /* Start of edge list for each vertex */ 1489 PetscInt *adjncy = adjacency; /* Edge lists for all vertices */ 1490 PetscInt *vwgt = NULL; /* Vertex weights */ 1491 PetscInt *adjwgt = NULL; /* Edge weights */ 1492 PetscInt wgtflag = 0; /* Indicates which weights are present */ 1493 PetscInt numflag = 0; /* Indicates initial offset (0 or 1) */ 1494 PetscInt ncon = 1; /* The number of weights per vertex */ 1495 PetscInt metis_ptype = pm->ptype; /* kway or recursive bisection */ 1496 real_t *tpwgts; /* The fraction of vertex weights assigned to each partition */ 1497 real_t *ubvec; /* The balance intolerance for vertex weights */ 1498 PetscInt options[64]; /* Options */ 1499 /* Outputs */ 1500 PetscInt v, i, *assignment, *points; 1501 PetscMPIInt size, rank, p; 1502 PetscErrorCode ierr; 1503 1504 PetscFunctionBegin; 1505 ierr = PetscObjectGetComm((PetscObject) part, &comm);CHKERRQ(ierr); 1506 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1507 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1508 /* Calculate vertex distribution */ 1509 ierr = PetscMalloc5(size+1,&vtxdist,nparts*ncon,&tpwgts,ncon,&ubvec,nvtxs,&assignment,nvtxs,&vwgt);CHKERRQ(ierr); 1510 vtxdist[0] = 0; 1511 ierr = MPI_Allgather(&nvtxs, 1, MPIU_INT, &vtxdist[1], 1, MPIU_INT, comm);CHKERRQ(ierr); 1512 for (p = 2; p <= size; ++p) { 1513 vtxdist[p] += vtxdist[p-1]; 1514 } 1515 /* Calculate partition weights */ 1516 for (p = 0; p < nparts; ++p) { 1517 tpwgts[p] = 1.0/nparts; 1518 } 1519 ubvec[0] = pm->imbalanceRatio; 1520 /* Weight cells by dofs on cell by default */ 1521 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 1522 if (section) { 1523 PetscInt cStart, cEnd, dof; 1524 1525 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1526 for (v = cStart; v < cEnd; ++v) { 1527 ierr = PetscSectionGetDof(section, v, &dof);CHKERRQ(ierr); 1528 /* WARNING: Assumes that meshes with overlap have the overlapped cells at the end of the stratum. */ 1529 /* To do this properly, we should use the cell numbering created in DMPlexCreatePartitionerGraph. */ 1530 if (v-cStart < numVertices) vwgt[v-cStart] = PetscMax(dof, 1); 1531 } 1532 } else { 1533 for (v = 0; v < nvtxs; ++v) vwgt[v] = 1; 1534 } 1535 wgtflag |= 2; /* have weights on graph vertices */ 1536 1537 if (nparts == 1) { 1538 ierr = PetscMemzero(assignment, nvtxs * sizeof(PetscInt));CHKERRQ(ierr); 1539 } else { 1540 for (p = 0; !vtxdist[p+1] && p < size; ++p); 1541 if (vtxdist[p+1] == vtxdist[size]) { 1542 if (rank == p) { 1543 ierr = METIS_SetDefaultOptions(options); /* initialize all defaults */ 1544 if (ierr != METIS_OK) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in METIS_SetDefaultOptions()"); 1545 if (metis_ptype == 1) { 1546 PetscStackPush("METIS_PartGraphRecursive"); 1547 ierr = METIS_PartGraphRecursive(&nvtxs, &ncon, xadj, adjncy, vwgt, NULL, adjwgt, &nparts, tpwgts, ubvec, options, &part->edgeCut, assignment); 1548 PetscStackPop; 1549 if (ierr != METIS_OK) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in METIS_PartGraphRecursive()"); 1550 } else { 1551 /* 1552 It would be nice to activate the two options below, but they would need some actual testing. 1553 - Turning on these options may exercise path of the METIS code that have bugs and may break production runs. 1554 - If CONTIG is set to 1, METIS will exit with error if the graph is disconnected, despite the manual saying the option is ignored in such case. 1555 */ 1556 /* options[METIS_OPTION_CONTIG] = 1; */ /* try to produce partitions that are contiguous */ 1557 /* options[METIS_OPTION_MINCONN] = 1; */ /* minimize the maximum degree of the subdomain graph */ 1558 PetscStackPush("METIS_PartGraphKway"); 1559 ierr = METIS_PartGraphKway(&nvtxs, &ncon, xadj, adjncy, vwgt, NULL, adjwgt, &nparts, tpwgts, ubvec, options, &part->edgeCut, assignment); 1560 PetscStackPop; 1561 if (ierr != METIS_OK) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in METIS_PartGraphKway()"); 1562 } 1563 } 1564 } else { 1565 options[0] = 1; 1566 options[1] = pm->debugFlag; 1567 PetscStackPush("ParMETIS_V3_PartKway"); 1568 ierr = ParMETIS_V3_PartKway(vtxdist, xadj, adjncy, vwgt, adjwgt, &wgtflag, &numflag, &ncon, &nparts, tpwgts, ubvec, options, &part->edgeCut, assignment, &comm); 1569 PetscStackPop; 1570 if (ierr != METIS_OK) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Error %d in ParMETIS_V3_PartKway()", ierr); 1571 } 1572 } 1573 /* Convert to PetscSection+IS */ 1574 ierr = PetscSectionSetChart(partSection, 0, nparts);CHKERRQ(ierr); 1575 for (v = 0; v < nvtxs; ++v) {ierr = PetscSectionAddDof(partSection, assignment[v], 1);CHKERRQ(ierr);} 1576 ierr = PetscSectionSetUp(partSection);CHKERRQ(ierr); 1577 ierr = PetscMalloc1(nvtxs, &points);CHKERRQ(ierr); 1578 for (p = 0, i = 0; p < nparts; ++p) { 1579 for (v = 0; v < nvtxs; ++v) { 1580 if (assignment[v] == p) points[i++] = v; 1581 } 1582 } 1583 if (i != nvtxs) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of points %D should be %D", i, nvtxs); 1584 ierr = ISCreateGeneral(comm, nvtxs, points, PETSC_OWN_POINTER, partition);CHKERRQ(ierr); 1585 ierr = PetscFree5(vtxdist,tpwgts,ubvec,assignment,vwgt);CHKERRQ(ierr); 1586 PetscFunctionReturn(0); 1587 #else 1588 SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_SUP, "Mesh partitioning needs external package support.\nPlease reconfigure with --download-parmetis."); 1589 #endif 1590 } 1591 1592 static PetscErrorCode PetscPartitionerInitialize_ParMetis(PetscPartitioner part) 1593 { 1594 PetscFunctionBegin; 1595 part->ops->view = PetscPartitionerView_ParMetis; 1596 part->ops->setfromoptions = PetscPartitionerSetFromOptions_ParMetis; 1597 part->ops->destroy = PetscPartitionerDestroy_ParMetis; 1598 part->ops->partition = PetscPartitionerPartition_ParMetis; 1599 PetscFunctionReturn(0); 1600 } 1601 1602 /*MC 1603 PETSCPARTITIONERPARMETIS = "parmetis" - A PetscPartitioner object using the ParMetis library 1604 1605 Level: intermediate 1606 1607 .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType() 1608 M*/ 1609 1610 PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_ParMetis(PetscPartitioner part) 1611 { 1612 PetscPartitioner_ParMetis *p; 1613 PetscErrorCode ierr; 1614 1615 PetscFunctionBegin; 1616 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 1617 ierr = PetscNewLog(part, &p);CHKERRQ(ierr); 1618 part->data = p; 1619 1620 p->ptype = 0; 1621 p->imbalanceRatio = 1.05; 1622 p->debugFlag = 0; 1623 1624 ierr = PetscPartitionerInitialize_ParMetis(part);CHKERRQ(ierr); 1625 ierr = PetscCitationsRegister(ParMetisPartitionerCitation, &ParMetisPartitionercite);CHKERRQ(ierr); 1626 PetscFunctionReturn(0); 1627 } 1628 1629 1630 PetscBool PTScotchPartitionercite = PETSC_FALSE; 1631 const char PTScotchPartitionerCitation[] = 1632 "@article{PTSCOTCH,\n" 1633 " author = {C. Chevalier and F. Pellegrini},\n" 1634 " title = {{PT-SCOTCH}: a tool for efficient parallel graph ordering},\n" 1635 " journal = {Parallel Computing},\n" 1636 " volume = {34},\n" 1637 " number = {6},\n" 1638 " pages = {318--331},\n" 1639 " year = {2008},\n" 1640 " doi = {https://doi.org/10.1016/j.parco.2007.12.001}\n" 1641 "}\n"; 1642 1643 typedef struct { 1644 PetscInt strategy; 1645 PetscReal imbalance; 1646 } PetscPartitioner_PTScotch; 1647 1648 static const char *const 1649 PTScotchStrategyList[] = { 1650 "DEFAULT", 1651 "QUALITY", 1652 "SPEED", 1653 "BALANCE", 1654 "SAFETY", 1655 "SCALABILITY", 1656 "RECURSIVE", 1657 "REMAP" 1658 }; 1659 1660 #if defined(PETSC_HAVE_PTSCOTCH) 1661 1662 EXTERN_C_BEGIN 1663 #include <ptscotch.h> 1664 EXTERN_C_END 1665 1666 #define CHKERRPTSCOTCH(ierr) do { if (ierr) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error calling PT-Scotch library"); } while(0) 1667 1668 static int PTScotch_Strategy(PetscInt strategy) 1669 { 1670 switch (strategy) { 1671 case 0: return SCOTCH_STRATDEFAULT; 1672 case 1: return SCOTCH_STRATQUALITY; 1673 case 2: return SCOTCH_STRATSPEED; 1674 case 3: return SCOTCH_STRATBALANCE; 1675 case 4: return SCOTCH_STRATSAFETY; 1676 case 5: return SCOTCH_STRATSCALABILITY; 1677 case 6: return SCOTCH_STRATRECURSIVE; 1678 case 7: return SCOTCH_STRATREMAP; 1679 default: return SCOTCH_STRATDEFAULT; 1680 } 1681 } 1682 1683 1684 static PetscErrorCode PTScotch_PartGraph_Seq(SCOTCH_Num strategy, double imbalance, SCOTCH_Num n, SCOTCH_Num xadj[], SCOTCH_Num adjncy[], 1685 SCOTCH_Num vtxwgt[], SCOTCH_Num adjwgt[], SCOTCH_Num nparts, SCOTCH_Num part[]) 1686 { 1687 SCOTCH_Graph grafdat; 1688 SCOTCH_Strat stradat; 1689 SCOTCH_Num vertnbr = n; 1690 SCOTCH_Num edgenbr = xadj[n]; 1691 SCOTCH_Num* velotab = vtxwgt; 1692 SCOTCH_Num* edlotab = adjwgt; 1693 SCOTCH_Num flagval = strategy; 1694 double kbalval = imbalance; 1695 PetscErrorCode ierr; 1696 1697 PetscFunctionBegin; 1698 { 1699 PetscBool flg = PETSC_TRUE; 1700 ierr = PetscOptionsGetBool(NULL, NULL, "-petscpartititoner_ptscotch_vertex_weight", &flg, NULL);CHKERRQ(ierr); 1701 if (!flg) velotab = NULL; 1702 } 1703 ierr = SCOTCH_graphInit(&grafdat);CHKERRPTSCOTCH(ierr); 1704 ierr = SCOTCH_graphBuild(&grafdat, 0, vertnbr, xadj, xadj + 1, velotab, NULL, edgenbr, adjncy, edlotab);CHKERRPTSCOTCH(ierr); 1705 ierr = SCOTCH_stratInit(&stradat);CHKERRPTSCOTCH(ierr); 1706 ierr = SCOTCH_stratGraphMapBuild(&stradat, flagval, nparts, kbalval);CHKERRPTSCOTCH(ierr); 1707 #if defined(PETSC_USE_DEBUG) 1708 ierr = SCOTCH_graphCheck(&grafdat);CHKERRPTSCOTCH(ierr); 1709 #endif 1710 ierr = SCOTCH_graphPart(&grafdat, nparts, &stradat, part);CHKERRPTSCOTCH(ierr); 1711 SCOTCH_stratExit(&stradat); 1712 SCOTCH_graphExit(&grafdat); 1713 PetscFunctionReturn(0); 1714 } 1715 1716 static PetscErrorCode PTScotch_PartGraph_MPI(SCOTCH_Num strategy, double imbalance, SCOTCH_Num vtxdist[], SCOTCH_Num xadj[], SCOTCH_Num adjncy[], 1717 SCOTCH_Num vtxwgt[], SCOTCH_Num adjwgt[], SCOTCH_Num nparts, SCOTCH_Num part[], MPI_Comm comm) 1718 { 1719 PetscMPIInt procglbnbr; 1720 PetscMPIInt proclocnum; 1721 SCOTCH_Arch archdat; 1722 SCOTCH_Dgraph grafdat; 1723 SCOTCH_Dmapping mappdat; 1724 SCOTCH_Strat stradat; 1725 SCOTCH_Num vertlocnbr; 1726 SCOTCH_Num edgelocnbr; 1727 SCOTCH_Num* veloloctab = vtxwgt; 1728 SCOTCH_Num* edloloctab = adjwgt; 1729 SCOTCH_Num flagval = strategy; 1730 double kbalval = imbalance; 1731 PetscErrorCode ierr; 1732 1733 PetscFunctionBegin; 1734 { 1735 PetscBool flg = PETSC_TRUE; 1736 ierr = PetscOptionsGetBool(NULL, NULL, "-petscpartititoner_ptscotch_vertex_weight", &flg, NULL);CHKERRQ(ierr); 1737 if (!flg) veloloctab = NULL; 1738 } 1739 ierr = MPI_Comm_size(comm, &procglbnbr);CHKERRQ(ierr); 1740 ierr = MPI_Comm_rank(comm, &proclocnum);CHKERRQ(ierr); 1741 vertlocnbr = vtxdist[proclocnum + 1] - vtxdist[proclocnum]; 1742 edgelocnbr = xadj[vertlocnbr]; 1743 1744 ierr = SCOTCH_dgraphInit(&grafdat, comm);CHKERRPTSCOTCH(ierr); 1745 ierr = SCOTCH_dgraphBuild(&grafdat, 0, vertlocnbr, vertlocnbr, xadj, xadj + 1, veloloctab, NULL, edgelocnbr, edgelocnbr, adjncy, NULL, edloloctab);CHKERRPTSCOTCH(ierr); 1746 #if defined(PETSC_USE_DEBUG) 1747 ierr = SCOTCH_dgraphCheck(&grafdat);CHKERRPTSCOTCH(ierr); 1748 #endif 1749 ierr = SCOTCH_stratInit(&stradat);CHKERRPTSCOTCH(ierr); 1750 ierr = SCOTCH_stratDgraphMapBuild(&stradat, flagval, procglbnbr, nparts, kbalval);CHKERRQ(ierr); 1751 ierr = SCOTCH_archInit(&archdat);CHKERRPTSCOTCH(ierr); 1752 ierr = SCOTCH_archCmplt(&archdat, nparts);CHKERRPTSCOTCH(ierr); 1753 ierr = SCOTCH_dgraphMapInit(&grafdat, &mappdat, &archdat, part);CHKERRPTSCOTCH(ierr); 1754 1755 ierr = SCOTCH_dgraphMapCompute(&grafdat, &mappdat, &stradat);CHKERRPTSCOTCH(ierr); 1756 SCOTCH_dgraphMapExit(&grafdat, &mappdat); 1757 SCOTCH_archExit(&archdat); 1758 SCOTCH_stratExit(&stradat); 1759 SCOTCH_dgraphExit(&grafdat); 1760 PetscFunctionReturn(0); 1761 } 1762 1763 #endif /* PETSC_HAVE_PTSCOTCH */ 1764 1765 static PetscErrorCode PetscPartitionerDestroy_PTScotch(PetscPartitioner part) 1766 { 1767 PetscPartitioner_PTScotch *p = (PetscPartitioner_PTScotch *) part->data; 1768 PetscErrorCode ierr; 1769 1770 PetscFunctionBegin; 1771 ierr = PetscFree(p);CHKERRQ(ierr); 1772 PetscFunctionReturn(0); 1773 } 1774 1775 static PetscErrorCode PetscPartitionerView_PTScotch_Ascii(PetscPartitioner part, PetscViewer viewer) 1776 { 1777 PetscPartitioner_PTScotch *p = (PetscPartitioner_PTScotch *) part->data; 1778 PetscErrorCode ierr; 1779 1780 PetscFunctionBegin; 1781 ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); 1782 ierr = PetscViewerASCIIPrintf(viewer, "using partitioning strategy %s\n",PTScotchStrategyList[p->strategy]);CHKERRQ(ierr); 1783 ierr = PetscViewerASCIIPrintf(viewer, "using load imbalance ratio %g\n",(double)p->imbalance);CHKERRQ(ierr); 1784 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 1785 PetscFunctionReturn(0); 1786 } 1787 1788 static PetscErrorCode PetscPartitionerView_PTScotch(PetscPartitioner part, PetscViewer viewer) 1789 { 1790 PetscBool iascii; 1791 PetscErrorCode ierr; 1792 1793 PetscFunctionBegin; 1794 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 1795 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 1796 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);CHKERRQ(ierr); 1797 if (iascii) {ierr = PetscPartitionerView_PTScotch_Ascii(part, viewer);CHKERRQ(ierr);} 1798 PetscFunctionReturn(0); 1799 } 1800 1801 static PetscErrorCode PetscPartitionerSetFromOptions_PTScotch(PetscOptionItems *PetscOptionsObject, PetscPartitioner part) 1802 { 1803 PetscPartitioner_PTScotch *p = (PetscPartitioner_PTScotch *) part->data; 1804 const char *const *slist = PTScotchStrategyList; 1805 PetscInt nlist = (PetscInt)(sizeof(PTScotchStrategyList)/sizeof(PTScotchStrategyList[0])); 1806 PetscBool flag; 1807 PetscErrorCode ierr; 1808 1809 PetscFunctionBegin; 1810 ierr = PetscOptionsHead(PetscOptionsObject, "PetscPartitioner PTScotch Options");CHKERRQ(ierr); 1811 ierr = PetscOptionsEList("-petscpartitioner_ptscotch_strategy","Partitioning strategy","",slist,nlist,slist[p->strategy],&p->strategy,&flag);CHKERRQ(ierr); 1812 ierr = PetscOptionsReal("-petscpartitioner_ptscotch_imbalance","Load imbalance ratio","",p->imbalance,&p->imbalance,&flag);CHKERRQ(ierr); 1813 ierr = PetscOptionsTail();CHKERRQ(ierr); 1814 PetscFunctionReturn(0); 1815 } 1816 1817 static PetscErrorCode PetscPartitionerPartition_PTScotch(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition) 1818 { 1819 #if defined(PETSC_HAVE_PTSCOTCH) 1820 MPI_Comm comm = PetscObjectComm((PetscObject)part); 1821 PetscInt nvtxs = numVertices; /* The number of vertices in full graph */ 1822 PetscInt *vtxdist; /* Distribution of vertices across processes */ 1823 PetscInt *xadj = start; /* Start of edge list for each vertex */ 1824 PetscInt *adjncy = adjacency; /* Edge lists for all vertices */ 1825 PetscInt *vwgt = NULL; /* Vertex weights */ 1826 PetscInt *adjwgt = NULL; /* Edge weights */ 1827 PetscInt v, i, *assignment, *points; 1828 PetscMPIInt size, rank, p; 1829 PetscErrorCode ierr; 1830 1831 PetscFunctionBegin; 1832 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1833 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1834 ierr = PetscMalloc2(nparts+1,&vtxdist,PetscMax(nvtxs,1),&assignment);CHKERRQ(ierr); 1835 1836 /* Calculate vertex distribution */ 1837 vtxdist[0] = 0; 1838 ierr = MPI_Allgather(&nvtxs, 1, MPIU_INT, &vtxdist[1], 1, MPIU_INT, comm);CHKERRQ(ierr); 1839 for (p = 2; p <= size; ++p) { 1840 vtxdist[p] += vtxdist[p-1]; 1841 } 1842 1843 if (nparts == 1) { 1844 ierr = PetscMemzero(assignment, nvtxs * sizeof(PetscInt));CHKERRQ(ierr); 1845 } else { 1846 PetscSection section; 1847 /* Weight cells by dofs on cell by default */ 1848 ierr = PetscMalloc1(PetscMax(nvtxs,1),&vwgt);CHKERRQ(ierr); 1849 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 1850 if (section) { 1851 PetscInt vStart, eEnd, dof; 1852 ierr = DMPlexGetHeightStratum(dm, 0, &vStart, &eEnd);CHKERRQ(ierr); 1853 for (v = vStart; v < eEnd; ++v) { 1854 ierr = PetscSectionGetDof(section, v, &dof);CHKERRQ(ierr); 1855 /* WARNING: Assumes that meshes with overlap have the overlapped cells at the end of the stratum. */ 1856 /* To do this properly, we should use the cell numbering created in DMPlexCreatePartitionerGraph. */ 1857 if (v-vStart < numVertices) vwgt[v-vStart] = PetscMax(dof, 1); 1858 } 1859 } else { 1860 for (v = 0; v < nvtxs; ++v) vwgt[v] = 1; 1861 } 1862 { 1863 PetscPartitioner_PTScotch *pts = (PetscPartitioner_PTScotch *) part->data; 1864 int strat = PTScotch_Strategy(pts->strategy); 1865 double imbal = (double)pts->imbalance; 1866 1867 for (p = 0; !vtxdist[p+1] && p < size; ++p); 1868 if (vtxdist[p+1] == vtxdist[size]) { 1869 if (rank == p) { 1870 ierr = PTScotch_PartGraph_Seq(strat, imbal, nvtxs, xadj, adjncy, vwgt, adjwgt, nparts, assignment);CHKERRQ(ierr); 1871 } 1872 } else { 1873 ierr = PTScotch_PartGraph_MPI(strat, imbal, vtxdist, xadj, adjncy, vwgt, adjwgt, nparts, assignment, comm);CHKERRQ(ierr); 1874 } 1875 } 1876 ierr = PetscFree(vwgt);CHKERRQ(ierr); 1877 } 1878 1879 /* Convert to PetscSection+IS */ 1880 ierr = PetscSectionSetChart(partSection, 0, nparts);CHKERRQ(ierr); 1881 for (v = 0; v < nvtxs; ++v) {ierr = PetscSectionAddDof(partSection, assignment[v], 1);CHKERRQ(ierr);} 1882 ierr = PetscSectionSetUp(partSection);CHKERRQ(ierr); 1883 ierr = PetscMalloc1(nvtxs, &points);CHKERRQ(ierr); 1884 for (p = 0, i = 0; p < nparts; ++p) { 1885 for (v = 0; v < nvtxs; ++v) { 1886 if (assignment[v] == p) points[i++] = v; 1887 } 1888 } 1889 if (i != nvtxs) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of points %D should be %D", i, nvtxs); 1890 ierr = ISCreateGeneral(comm, nvtxs, points, PETSC_OWN_POINTER, partition);CHKERRQ(ierr); 1891 1892 ierr = PetscFree2(vtxdist,assignment);CHKERRQ(ierr); 1893 PetscFunctionReturn(0); 1894 #else 1895 SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_SUP, "Mesh partitioning needs external package support.\nPlease reconfigure with --download-ptscotch."); 1896 #endif 1897 } 1898 1899 static PetscErrorCode PetscPartitionerInitialize_PTScotch(PetscPartitioner part) 1900 { 1901 PetscFunctionBegin; 1902 part->ops->view = PetscPartitionerView_PTScotch; 1903 part->ops->destroy = PetscPartitionerDestroy_PTScotch; 1904 part->ops->partition = PetscPartitionerPartition_PTScotch; 1905 part->ops->setfromoptions = PetscPartitionerSetFromOptions_PTScotch; 1906 PetscFunctionReturn(0); 1907 } 1908 1909 /*MC 1910 PETSCPARTITIONERPTSCOTCH = "ptscotch" - A PetscPartitioner object using the PT-Scotch library 1911 1912 Level: intermediate 1913 1914 .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType() 1915 M*/ 1916 1917 PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_PTScotch(PetscPartitioner part) 1918 { 1919 PetscPartitioner_PTScotch *p; 1920 PetscErrorCode ierr; 1921 1922 PetscFunctionBegin; 1923 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 1924 ierr = PetscNewLog(part, &p);CHKERRQ(ierr); 1925 part->data = p; 1926 1927 p->strategy = 0; 1928 p->imbalance = 0.01; 1929 1930 ierr = PetscPartitionerInitialize_PTScotch(part);CHKERRQ(ierr); 1931 ierr = PetscCitationsRegister(PTScotchPartitionerCitation, &PTScotchPartitionercite);CHKERRQ(ierr); 1932 PetscFunctionReturn(0); 1933 } 1934 1935 1936 /*@ 1937 DMPlexGetPartitioner - Get the mesh partitioner 1938 1939 Not collective 1940 1941 Input Parameter: 1942 . dm - The DM 1943 1944 Output Parameter: 1945 . part - The PetscPartitioner 1946 1947 Level: developer 1948 1949 Note: This gets a borrowed reference, so the user should not destroy this PetscPartitioner. 1950 1951 .seealso DMPlexDistribute(), DMPlexSetPartitioner(), PetscPartitionerCreate() 1952 @*/ 1953 PetscErrorCode DMPlexGetPartitioner(DM dm, PetscPartitioner *part) 1954 { 1955 DM_Plex *mesh = (DM_Plex *) dm->data; 1956 1957 PetscFunctionBegin; 1958 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1959 PetscValidPointer(part, 2); 1960 *part = mesh->partitioner; 1961 PetscFunctionReturn(0); 1962 } 1963 1964 /*@ 1965 DMPlexSetPartitioner - Set the mesh partitioner 1966 1967 logically collective on dm and part 1968 1969 Input Parameters: 1970 + dm - The DM 1971 - part - The partitioner 1972 1973 Level: developer 1974 1975 Note: Any existing PetscPartitioner will be destroyed. 1976 1977 .seealso DMPlexDistribute(), DMPlexGetPartitioner(), PetscPartitionerCreate() 1978 @*/ 1979 PetscErrorCode DMPlexSetPartitioner(DM dm, PetscPartitioner part) 1980 { 1981 DM_Plex *mesh = (DM_Plex *) dm->data; 1982 PetscErrorCode ierr; 1983 1984 PetscFunctionBegin; 1985 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1986 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 2); 1987 ierr = PetscObjectReference((PetscObject)part);CHKERRQ(ierr); 1988 ierr = PetscPartitionerDestroy(&mesh->partitioner);CHKERRQ(ierr); 1989 mesh->partitioner = part; 1990 PetscFunctionReturn(0); 1991 } 1992 1993 static PetscErrorCode DMPlexAddClosure_Tree(DM dm, PetscHSetI ht, PetscInt point, PetscBool up, PetscBool down) 1994 { 1995 PetscErrorCode ierr; 1996 1997 PetscFunctionBegin; 1998 if (up) { 1999 PetscInt parent; 2000 2001 ierr = DMPlexGetTreeParent(dm,point,&parent,NULL);CHKERRQ(ierr); 2002 if (parent != point) { 2003 PetscInt closureSize, *closure = NULL, i; 2004 2005 ierr = DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 2006 for (i = 0; i < closureSize; i++) { 2007 PetscInt cpoint = closure[2*i]; 2008 2009 ierr = PetscHSetIAdd(ht, cpoint);CHKERRQ(ierr); 2010 ierr = DMPlexAddClosure_Tree(dm,ht,cpoint,PETSC_TRUE,PETSC_FALSE);CHKERRQ(ierr); 2011 } 2012 ierr = DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);CHKERRQ(ierr); 2013 } 2014 } 2015 if (down) { 2016 PetscInt numChildren; 2017 const PetscInt *children; 2018 2019 ierr = DMPlexGetTreeChildren(dm,point,&numChildren,&children);CHKERRQ(ierr); 2020 if (numChildren) { 2021 PetscInt i; 2022 2023 for (i = 0; i < numChildren; i++) { 2024 PetscInt cpoint = children[i]; 2025 2026 ierr = PetscHSetIAdd(ht, cpoint);CHKERRQ(ierr); 2027 ierr = DMPlexAddClosure_Tree(dm,ht,cpoint,PETSC_FALSE,PETSC_TRUE);CHKERRQ(ierr); 2028 } 2029 } 2030 } 2031 PetscFunctionReturn(0); 2032 } 2033 2034 /*@ 2035 DMPlexPartitionLabelClosure - Add the closure of all points to the partition label 2036 2037 Input Parameters: 2038 + dm - The DM 2039 - label - DMLabel assinging ranks to remote roots 2040 2041 Level: developer 2042 2043 .seealso: DMPlexPartitionLabelCreateSF, DMPlexDistribute(), DMPlexCreateOverlap 2044 @*/ 2045 PetscErrorCode DMPlexPartitionLabelClosure(DM dm, DMLabel label) 2046 { 2047 IS rankIS, pointIS; 2048 const PetscInt *ranks, *points; 2049 PetscInt numRanks, numPoints, r, p, c, closureSize; 2050 PetscInt *closure = NULL; 2051 DM_Plex *mesh = (DM_Plex *)dm->data; 2052 PetscBool hasTree = (mesh->parentSection || mesh->childSection) ? PETSC_TRUE : PETSC_FALSE; 2053 PetscErrorCode ierr; 2054 2055 PetscFunctionBegin; 2056 ierr = DMLabelGetValueIS(label, &rankIS);CHKERRQ(ierr); 2057 ierr = ISGetLocalSize(rankIS, &numRanks);CHKERRQ(ierr); 2058 ierr = ISGetIndices(rankIS, &ranks);CHKERRQ(ierr); 2059 2060 for (r = 0; r < numRanks; ++r) { 2061 const PetscInt rank = ranks[r]; 2062 PetscHSetI ht; 2063 PetscInt nelems, *elems, off = 0; 2064 2065 ierr = DMLabelGetStratumIS(label, rank, &pointIS);CHKERRQ(ierr); 2066 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 2067 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2068 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 2069 ierr = PetscHSetIResize(ht, numPoints*16);CHKERRQ(ierr); 2070 for (p = 0; p < numPoints; ++p) { 2071 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 2072 for (c = 0; c < closureSize*2; c += 2) { 2073 ierr = PetscHSetIAdd(ht, closure[c]);CHKERRQ(ierr); 2074 if (hasTree) {ierr = DMPlexAddClosure_Tree(dm, ht, closure[c], PETSC_TRUE, PETSC_TRUE);CHKERRQ(ierr);} 2075 } 2076 } 2077 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2078 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2079 ierr = PetscHSetIGetSize(ht, &nelems);CHKERRQ(ierr); 2080 ierr = PetscMalloc1(nelems, &elems);CHKERRQ(ierr); 2081 ierr = PetscHSetIGetElems(ht, &off, elems);CHKERRQ(ierr); 2082 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 2083 ierr = PetscSortInt(nelems, elems);CHKERRQ(ierr); 2084 ierr = ISCreateGeneral(PETSC_COMM_SELF, nelems, elems, PETSC_OWN_POINTER, &pointIS);CHKERRQ(ierr); 2085 ierr = DMLabelSetStratumIS(label, rank, pointIS);CHKERRQ(ierr); 2086 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2087 } 2088 2089 if (closure) {ierr = DMPlexRestoreTransitiveClosure(dm, 0, PETSC_TRUE, NULL, &closure);CHKERRQ(ierr);} 2090 ierr = ISRestoreIndices(rankIS, &ranks);CHKERRQ(ierr); 2091 ierr = ISDestroy(&rankIS);CHKERRQ(ierr); 2092 PetscFunctionReturn(0); 2093 } 2094 2095 /*@ 2096 DMPlexPartitionLabelAdjacency - Add one level of adjacent points to the partition label 2097 2098 Input Parameters: 2099 + dm - The DM 2100 - label - DMLabel assinging ranks to remote roots 2101 2102 Level: developer 2103 2104 .seealso: DMPlexPartitionLabelCreateSF, DMPlexDistribute(), DMPlexCreateOverlap 2105 @*/ 2106 PetscErrorCode DMPlexPartitionLabelAdjacency(DM dm, DMLabel label) 2107 { 2108 IS rankIS, pointIS; 2109 const PetscInt *ranks, *points; 2110 PetscInt numRanks, numPoints, r, p, a, adjSize; 2111 PetscInt *adj = NULL; 2112 PetscErrorCode ierr; 2113 2114 PetscFunctionBegin; 2115 ierr = DMLabelGetValueIS(label, &rankIS);CHKERRQ(ierr); 2116 ierr = ISGetLocalSize(rankIS, &numRanks);CHKERRQ(ierr); 2117 ierr = ISGetIndices(rankIS, &ranks);CHKERRQ(ierr); 2118 for (r = 0; r < numRanks; ++r) { 2119 const PetscInt rank = ranks[r]; 2120 2121 ierr = DMLabelGetStratumIS(label, rank, &pointIS);CHKERRQ(ierr); 2122 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 2123 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2124 for (p = 0; p < numPoints; ++p) { 2125 adjSize = PETSC_DETERMINE; 2126 ierr = DMPlexGetAdjacency(dm, points[p], &adjSize, &adj);CHKERRQ(ierr); 2127 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(label, adj[a], rank);CHKERRQ(ierr);} 2128 } 2129 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2130 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2131 } 2132 ierr = ISRestoreIndices(rankIS, &ranks);CHKERRQ(ierr); 2133 ierr = ISDestroy(&rankIS);CHKERRQ(ierr); 2134 ierr = PetscFree(adj);CHKERRQ(ierr); 2135 PetscFunctionReturn(0); 2136 } 2137 2138 /*@ 2139 DMPlexPartitionLabelPropagate - Propagate points in a partition label over the point SF 2140 2141 Input Parameters: 2142 + dm - The DM 2143 - label - DMLabel assinging ranks to remote roots 2144 2145 Level: developer 2146 2147 Note: This is required when generating multi-level overlaps to capture 2148 overlap points from non-neighbouring partitions. 2149 2150 .seealso: DMPlexPartitionLabelCreateSF, DMPlexDistribute(), DMPlexCreateOverlap 2151 @*/ 2152 PetscErrorCode DMPlexPartitionLabelPropagate(DM dm, DMLabel label) 2153 { 2154 MPI_Comm comm; 2155 PetscMPIInt rank; 2156 PetscSF sfPoint; 2157 DMLabel lblRoots, lblLeaves; 2158 IS rankIS, pointIS; 2159 const PetscInt *ranks; 2160 PetscInt numRanks, r; 2161 PetscErrorCode ierr; 2162 2163 PetscFunctionBegin; 2164 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 2165 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 2166 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2167 /* Pull point contributions from remote leaves into local roots */ 2168 ierr = DMLabelGather(label, sfPoint, &lblLeaves);CHKERRQ(ierr); 2169 ierr = DMLabelGetValueIS(lblLeaves, &rankIS);CHKERRQ(ierr); 2170 ierr = ISGetLocalSize(rankIS, &numRanks);CHKERRQ(ierr); 2171 ierr = ISGetIndices(rankIS, &ranks);CHKERRQ(ierr); 2172 for (r = 0; r < numRanks; ++r) { 2173 const PetscInt remoteRank = ranks[r]; 2174 if (remoteRank == rank) continue; 2175 ierr = DMLabelGetStratumIS(lblLeaves, remoteRank, &pointIS);CHKERRQ(ierr); 2176 ierr = DMLabelInsertIS(label, pointIS, remoteRank);CHKERRQ(ierr); 2177 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2178 } 2179 ierr = ISRestoreIndices(rankIS, &ranks);CHKERRQ(ierr); 2180 ierr = ISDestroy(&rankIS);CHKERRQ(ierr); 2181 ierr = DMLabelDestroy(&lblLeaves);CHKERRQ(ierr); 2182 /* Push point contributions from roots into remote leaves */ 2183 ierr = DMLabelDistribute(label, sfPoint, &lblRoots);CHKERRQ(ierr); 2184 ierr = DMLabelGetValueIS(lblRoots, &rankIS);CHKERRQ(ierr); 2185 ierr = ISGetLocalSize(rankIS, &numRanks);CHKERRQ(ierr); 2186 ierr = ISGetIndices(rankIS, &ranks);CHKERRQ(ierr); 2187 for (r = 0; r < numRanks; ++r) { 2188 const PetscInt remoteRank = ranks[r]; 2189 if (remoteRank == rank) continue; 2190 ierr = DMLabelGetStratumIS(lblRoots, remoteRank, &pointIS);CHKERRQ(ierr); 2191 ierr = DMLabelInsertIS(label, pointIS, remoteRank);CHKERRQ(ierr); 2192 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2193 } 2194 ierr = ISRestoreIndices(rankIS, &ranks);CHKERRQ(ierr); 2195 ierr = ISDestroy(&rankIS);CHKERRQ(ierr); 2196 ierr = DMLabelDestroy(&lblRoots);CHKERRQ(ierr); 2197 PetscFunctionReturn(0); 2198 } 2199 2200 /*@ 2201 DMPlexPartitionLabelInvert - Create a partition label of remote roots from a local root label 2202 2203 Input Parameters: 2204 + dm - The DM 2205 . rootLabel - DMLabel assinging ranks to local roots 2206 . processSF - A star forest mapping into the local index on each remote rank 2207 2208 Output Parameter: 2209 - leafLabel - DMLabel assinging ranks to remote roots 2210 2211 Note: The rootLabel defines a send pattern by mapping local points to remote target ranks. The 2212 resulting leafLabel is a receiver mapping of remote roots to their parent rank. 2213 2214 Level: developer 2215 2216 .seealso: DMPlexPartitionLabelCreateSF, DMPlexDistribute(), DMPlexCreateOverlap 2217 @*/ 2218 PetscErrorCode DMPlexPartitionLabelInvert(DM dm, DMLabel rootLabel, PetscSF processSF, DMLabel leafLabel) 2219 { 2220 MPI_Comm comm; 2221 PetscMPIInt rank, size; 2222 PetscInt p, n, numNeighbors, ssize, l, nleaves; 2223 PetscSF sfPoint; 2224 PetscSFNode *rootPoints, *leafPoints; 2225 PetscSection rootSection, leafSection; 2226 const PetscSFNode *remote; 2227 const PetscInt *local, *neighbors; 2228 IS valueIS; 2229 PetscErrorCode ierr; 2230 2231 PetscFunctionBegin; 2232 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 2233 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 2234 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 2235 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2236 2237 /* Convert to (point, rank) and use actual owners */ 2238 ierr = PetscSectionCreate(comm, &rootSection);CHKERRQ(ierr); 2239 ierr = PetscSectionSetChart(rootSection, 0, size);CHKERRQ(ierr); 2240 ierr = DMLabelGetValueIS(rootLabel, &valueIS);CHKERRQ(ierr); 2241 ierr = ISGetLocalSize(valueIS, &numNeighbors);CHKERRQ(ierr); 2242 ierr = ISGetIndices(valueIS, &neighbors);CHKERRQ(ierr); 2243 for (n = 0; n < numNeighbors; ++n) { 2244 PetscInt numPoints; 2245 2246 ierr = DMLabelGetStratumSize(rootLabel, neighbors[n], &numPoints);CHKERRQ(ierr); 2247 ierr = PetscSectionAddDof(rootSection, neighbors[n], numPoints);CHKERRQ(ierr); 2248 } 2249 ierr = PetscSectionSetUp(rootSection);CHKERRQ(ierr); 2250 ierr = PetscSectionGetStorageSize(rootSection, &ssize);CHKERRQ(ierr); 2251 ierr = PetscMalloc1(ssize, &rootPoints);CHKERRQ(ierr); 2252 ierr = PetscSFGetGraph(sfPoint, NULL, &nleaves, &local, &remote);CHKERRQ(ierr); 2253 for (n = 0; n < numNeighbors; ++n) { 2254 IS pointIS; 2255 const PetscInt *points; 2256 PetscInt off, numPoints, p; 2257 2258 ierr = PetscSectionGetOffset(rootSection, neighbors[n], &off);CHKERRQ(ierr); 2259 ierr = DMLabelGetStratumIS(rootLabel, neighbors[n], &pointIS);CHKERRQ(ierr); 2260 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 2261 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2262 for (p = 0; p < numPoints; ++p) { 2263 if (local) {ierr = PetscFindInt(points[p], nleaves, local, &l);CHKERRQ(ierr);} 2264 else {l = -1;} 2265 if (l >= 0) {rootPoints[off+p] = remote[l];} 2266 else {rootPoints[off+p].index = points[p]; rootPoints[off+p].rank = rank;} 2267 } 2268 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2269 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2270 } 2271 ierr = ISRestoreIndices(valueIS, &neighbors);CHKERRQ(ierr); 2272 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 2273 /* Communicate overlap */ 2274 ierr = PetscSectionCreate(comm, &leafSection);CHKERRQ(ierr); 2275 ierr = DMPlexDistributeData(dm, processSF, rootSection, MPIU_2INT, rootPoints, leafSection, (void**) &leafPoints);CHKERRQ(ierr); 2276 /* Filter remote contributions (ovLeafPoints) into the overlapSF */ 2277 ierr = PetscSectionGetStorageSize(leafSection, &ssize);CHKERRQ(ierr); 2278 for (p = 0; p < ssize; p++) { 2279 ierr = DMLabelSetValue(leafLabel, leafPoints[p].index, leafPoints[p].rank);CHKERRQ(ierr); 2280 } 2281 ierr = PetscFree(rootPoints);CHKERRQ(ierr); 2282 ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr); 2283 ierr = PetscFree(leafPoints);CHKERRQ(ierr); 2284 ierr = PetscSectionDestroy(&leafSection);CHKERRQ(ierr); 2285 PetscFunctionReturn(0); 2286 } 2287 2288 /*@ 2289 DMPlexPartitionLabelCreateSF - Create a star forest from a label that assigns ranks to points 2290 2291 Input Parameters: 2292 + dm - The DM 2293 . label - DMLabel assinging ranks to remote roots 2294 2295 Output Parameter: 2296 - sf - The star forest communication context encapsulating the defined mapping 2297 2298 Note: The incoming label is a receiver mapping of remote points to their parent rank. 2299 2300 Level: developer 2301 2302 .seealso: DMPlexDistribute(), DMPlexCreateOverlap 2303 @*/ 2304 PetscErrorCode DMPlexPartitionLabelCreateSF(DM dm, DMLabel label, PetscSF *sf) 2305 { 2306 PetscMPIInt rank, size; 2307 PetscInt n, numRemote, p, numPoints, pStart, pEnd, idx = 0; 2308 PetscSFNode *remotePoints; 2309 IS remoteRootIS; 2310 const PetscInt *remoteRoots; 2311 PetscErrorCode ierr; 2312 2313 PetscFunctionBegin; 2314 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2315 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 2316 2317 for (numRemote = 0, n = 0; n < size; ++n) { 2318 ierr = DMLabelGetStratumSize(label, n, &numPoints);CHKERRQ(ierr); 2319 numRemote += numPoints; 2320 } 2321 ierr = PetscMalloc1(numRemote, &remotePoints);CHKERRQ(ierr); 2322 /* Put owned points first */ 2323 ierr = DMLabelGetStratumSize(label, rank, &numPoints);CHKERRQ(ierr); 2324 if (numPoints > 0) { 2325 ierr = DMLabelGetStratumIS(label, rank, &remoteRootIS);CHKERRQ(ierr); 2326 ierr = ISGetIndices(remoteRootIS, &remoteRoots);CHKERRQ(ierr); 2327 for (p = 0; p < numPoints; p++) { 2328 remotePoints[idx].index = remoteRoots[p]; 2329 remotePoints[idx].rank = rank; 2330 idx++; 2331 } 2332 ierr = ISRestoreIndices(remoteRootIS, &remoteRoots);CHKERRQ(ierr); 2333 ierr = ISDestroy(&remoteRootIS);CHKERRQ(ierr); 2334 } 2335 /* Now add remote points */ 2336 for (n = 0; n < size; ++n) { 2337 ierr = DMLabelGetStratumSize(label, n, &numPoints);CHKERRQ(ierr); 2338 if (numPoints <= 0 || n == rank) continue; 2339 ierr = DMLabelGetStratumIS(label, n, &remoteRootIS);CHKERRQ(ierr); 2340 ierr = ISGetIndices(remoteRootIS, &remoteRoots);CHKERRQ(ierr); 2341 for (p = 0; p < numPoints; p++) { 2342 remotePoints[idx].index = remoteRoots[p]; 2343 remotePoints[idx].rank = n; 2344 idx++; 2345 } 2346 ierr = ISRestoreIndices(remoteRootIS, &remoteRoots);CHKERRQ(ierr); 2347 ierr = ISDestroy(&remoteRootIS);CHKERRQ(ierr); 2348 } 2349 ierr = PetscSFCreate(PetscObjectComm((PetscObject) dm), sf);CHKERRQ(ierr); 2350 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2351 ierr = PetscSFSetGraph(*sf, pEnd-pStart, numRemote, NULL, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 2352 PetscFunctionReturn(0); 2353 } 2354 2355 /*@ 2356 2357 DMPlexRewriteSF - Rewrites the ownership of the SF of a DM (in place). 2358 2359 Input parameters: 2360 + dm - The DMPlex object. 2361 + n - The number of points. 2362 + pointsToRewrite - The points in the SF whose ownership will change. 2363 + targetOwners - New owner for each element in pointsToRewrite. 2364 + degrees - Degrees of the points in the SF as obtained by PetscSFComputeDegreeBegin/PetscSFComputeDegreeEnd. 2365 2366 Level: developer 2367 2368 @*/ 2369 static PetscErrorCode DMPlexRewriteSF(DM dm, PetscInt n, PetscInt *pointsToRewrite, PetscInt *targetOwners, const PetscInt *degrees) 2370 { 2371 PetscInt ierr, pStart, pEnd, i, j, counter, leafCounter, sumDegrees, nroots, nleafs; 2372 PetscInt *cumSumDegrees, *newOwners, *newNumbers, *rankOnLeafs, *locationsOfLeafs, *remoteLocalPointOfLeafs, *points, *leafsNew; 2373 PetscSFNode *leafLocationsNew; 2374 const PetscSFNode *iremote; 2375 const PetscInt *ilocal; 2376 PetscBool *isLeaf; 2377 PetscSF sf; 2378 MPI_Comm comm; 2379 PetscMPIInt rank, size; 2380 2381 PetscFunctionBegin; 2382 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 2383 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 2384 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 2385 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2386 2387 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2388 ierr = PetscSFGetGraph(sf, &nroots, &nleafs, &ilocal, &iremote); CHKERRQ(ierr); 2389 ierr = PetscMalloc1(pEnd-pStart, &isLeaf);CHKERRQ(ierr); 2390 for (i=0; i<pEnd-pStart; i++) { 2391 isLeaf[i] = PETSC_FALSE; 2392 } 2393 for (i=0; i<nleafs; i++) { 2394 isLeaf[ilocal[i]-pStart] = PETSC_TRUE; 2395 } 2396 2397 ierr = PetscMalloc1(pEnd-pStart+1, &cumSumDegrees);CHKERRQ(ierr); 2398 cumSumDegrees[0] = 0; 2399 for (i=1; i<=pEnd-pStart; i++) { 2400 cumSumDegrees[i] = cumSumDegrees[i-1] + degrees[i-1]; 2401 } 2402 sumDegrees = cumSumDegrees[pEnd-pStart]; 2403 /* get the location of my leafs (we have sumDegrees many leafs pointing at our roots) */ 2404 2405 ierr = PetscMalloc1(sumDegrees, &locationsOfLeafs);CHKERRQ(ierr); 2406 ierr = PetscMalloc1(pEnd-pStart, &rankOnLeafs);CHKERRQ(ierr); 2407 for (i=0; i<pEnd-pStart; i++) { 2408 rankOnLeafs[i] = rank; 2409 } 2410 ierr = PetscSFGatherBegin(sf, MPIU_INT, rankOnLeafs, locationsOfLeafs);CHKERRQ(ierr); 2411 ierr = PetscSFGatherEnd(sf, MPIU_INT, rankOnLeafs, locationsOfLeafs);CHKERRQ(ierr); 2412 ierr = PetscFree(rankOnLeafs);CHKERRQ(ierr); 2413 2414 /* get the remote local points of my leaves */ 2415 ierr = PetscMalloc1(sumDegrees, &remoteLocalPointOfLeafs);CHKERRQ(ierr); 2416 ierr = PetscMalloc1(pEnd-pStart, &points);CHKERRQ(ierr); 2417 for (i=0; i<pEnd-pStart; i++) { 2418 points[i] = pStart+i; 2419 } 2420 ierr = PetscSFGatherBegin(sf, MPIU_INT, points, remoteLocalPointOfLeafs);CHKERRQ(ierr); 2421 ierr = PetscSFGatherEnd(sf, MPIU_INT, points, remoteLocalPointOfLeafs);CHKERRQ(ierr); 2422 ierr = PetscFree(points);CHKERRQ(ierr); 2423 /* Figure out the new owners of the vertices that are up for grabs and their numbers on the new owners */ 2424 ierr = PetscMalloc1(pEnd-pStart, &newOwners);CHKERRQ(ierr); 2425 ierr = PetscMalloc1(pEnd-pStart, &newNumbers);CHKERRQ(ierr); 2426 for (i=0; i<pEnd-pStart; i++) { 2427 newOwners[i] = -1; 2428 newNumbers[i] = -1; 2429 } 2430 { 2431 PetscInt oldNumber, newNumber, oldOwner, newOwner; 2432 for (i=0; i<n; i++) { 2433 oldNumber = pointsToRewrite[i]; 2434 newNumber = -1; 2435 oldOwner = rank; 2436 newOwner = targetOwners[i]; 2437 if (oldOwner == newOwner) { 2438 newNumber = oldNumber; 2439 } else { 2440 for (j=0; j<degrees[oldNumber]; j++) { 2441 if (locationsOfLeafs[cumSumDegrees[oldNumber]+j] == newOwner) { 2442 newNumber = remoteLocalPointOfLeafs[cumSumDegrees[oldNumber]+j]; 2443 break; 2444 } 2445 } 2446 } 2447 if (newNumber == -1) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Couldn't find the new owner of vertex."); 2448 2449 newOwners[oldNumber] = newOwner; 2450 newNumbers[oldNumber] = newNumber; 2451 } 2452 } 2453 ierr = PetscFree(cumSumDegrees);CHKERRQ(ierr); 2454 ierr = PetscFree(locationsOfLeafs);CHKERRQ(ierr); 2455 ierr = PetscFree(remoteLocalPointOfLeafs);CHKERRQ(ierr); 2456 2457 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2458 ierr = PetscSFBcastBegin(sf, MPIU_INT, newOwners, newOwners);CHKERRQ(ierr); 2459 ierr = PetscSFBcastEnd(sf, MPIU_INT, newOwners, newOwners);CHKERRQ(ierr); 2460 ierr = PetscSFBcastBegin(sf, MPIU_INT, newNumbers, newNumbers);CHKERRQ(ierr); 2461 ierr = PetscSFBcastEnd(sf, MPIU_INT, newNumbers, newNumbers);CHKERRQ(ierr); 2462 2463 /* Now count how many leafs we have on each processor. */ 2464 leafCounter=0; 2465 for (i=0; i<pEnd-pStart; i++) { 2466 if (newOwners[i] >= 0) { 2467 if(newOwners[i] != rank) { 2468 leafCounter++; 2469 } 2470 } else { 2471 if (isLeaf[i]) { 2472 leafCounter++; 2473 } 2474 } 2475 } 2476 2477 /* Now set up the new sf by creating the leaf arrays */ 2478 ierr = PetscMalloc1(leafCounter, &leafsNew);CHKERRQ(ierr); 2479 ierr = PetscMalloc1(leafCounter, &leafLocationsNew);CHKERRQ(ierr); 2480 2481 leafCounter = 0; 2482 counter = 0; 2483 for (i=0; i<pEnd-pStart; i++) { 2484 if (newOwners[i] >= 0) { 2485 if(newOwners[i] != rank) { 2486 leafsNew[leafCounter] = i; 2487 leafLocationsNew[leafCounter].rank = newOwners[i]; 2488 leafLocationsNew[leafCounter].index = newNumbers[i]; 2489 leafCounter++; 2490 } 2491 } else { 2492 if (isLeaf[i]) { 2493 leafsNew[leafCounter] = i; 2494 leafLocationsNew[leafCounter].rank = iremote[counter].rank; 2495 leafLocationsNew[leafCounter].index = iremote[counter].index; 2496 leafCounter++; 2497 } 2498 } 2499 if(isLeaf[i]) { 2500 counter++; 2501 } 2502 } 2503 2504 ierr = PetscSFSetGraph(sf, nroots, leafCounter, leafsNew, PETSC_OWN_POINTER, leafLocationsNew, PETSC_OWN_POINTER);CHKERRQ(ierr); 2505 ierr = PetscFree(newOwners);CHKERRQ(ierr); 2506 ierr = PetscFree(newNumbers);CHKERRQ(ierr); 2507 ierr = PetscFree(isLeaf);CHKERRQ(ierr); 2508 PetscFunctionReturn(0); 2509 } 2510 2511 static PetscErrorCode DMPlexViewDistribution(MPI_Comm comm, PetscInt n, PetscInt skip, PetscInt *vtxwgt, PetscInt *part, PetscViewer viewer) 2512 { 2513 PetscInt *distribution, min, max, sum, i, ierr; 2514 PetscMPIInt rank, size; 2515 PetscFunctionBegin; 2516 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 2517 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 2518 ierr = PetscCalloc1(size, &distribution);CHKERRQ(ierr); 2519 for (i=0; i<n; i++) { 2520 if (part) distribution[part[i]] += vtxwgt[skip*i]; 2521 else distribution[rank] += vtxwgt[skip*i]; 2522 } 2523 ierr = MPI_Allreduce(MPI_IN_PLACE, distribution, size, MPIU_INT, MPI_SUM, comm);CHKERRQ(ierr); 2524 min = distribution[0]; 2525 max = distribution[0]; 2526 sum = distribution[0]; 2527 for (i=1; i<size; i++) { 2528 if (distribution[i]<min) min=distribution[i]; 2529 if (distribution[i]>max) max=distribution[i]; 2530 sum += distribution[i]; 2531 } 2532 ierr = PetscViewerASCIIPrintf(viewer, "Min: %D, Avg: %D, Max: %D, Balance: %f\n", min, sum/size, max, (max*1.*size)/sum);CHKERRQ(ierr); 2533 ierr = PetscFree(distribution);CHKERRQ(ierr); 2534 PetscFunctionReturn(0); 2535 } 2536 2537 /*@ 2538 DMPlexRebalanceSharedPoints - Redistribute points in the plex that are shared in order to achieve better balancing. This routine updates the PointSF of the DM inplace. 2539 2540 Input parameters: 2541 + dm - The DMPlex object. 2542 + entityDepth - depth of the entity to balance (0 -> balance vertices). 2543 + useInitialGuess - whether to use the current distribution as initial guess (only used by ParMETIS). 2544 + parallel - whether to use ParMETIS and do the partition in parallel or whether to gather the graph onto a single process and use METIS. 2545 2546 Level: user 2547 2548 @*/ 2549 2550 PetscErrorCode DMPlexRebalanceSharedPoints(DM dm, PetscInt entityDepth, PetscBool useInitialGuess, PetscBool parallel) 2551 { 2552 #if defined(PETSC_HAVE_PARMETIS) 2553 PetscSF sf; 2554 PetscInt ierr, i, j; 2555 PetscInt eBegin, eEnd, nroots, nleafs, pStart, pEnd; 2556 const PetscInt *degrees, *ilocal; 2557 const PetscSFNode *iremote; 2558 PetscBool *toBalance, *isLeaf, *isExclusivelyOwned, *isNonExclusivelyOwned; 2559 PetscInt numExclusivelyOwned, numNonExclusivelyOwned; 2560 PetscMPIInt rank, size; 2561 PetscInt *globalNumbersOfLocalOwnedVertices, *leafGlobalNumbers; 2562 const PetscInt *cumSumVertices; 2563 PetscInt offset, counter; 2564 PetscInt lenadjncy; 2565 PetscInt *xadj, *adjncy, *vtxwgt; 2566 PetscInt lenxadj; 2567 PetscInt *adjwgt = NULL; 2568 PetscInt *part, *options; 2569 PetscInt nparts, wgtflag, numflag, ncon, edgecut; 2570 real_t *ubvec; 2571 PetscInt *firstVertices, *renumbering; 2572 PetscInt failed, failedGlobal; 2573 MPI_Comm comm; 2574 Mat A, Apre; 2575 PetscScalar one = 1; 2576 const char *prefix = NULL; 2577 PetscViewer viewer; 2578 PetscViewerFormat format; 2579 PetscLayout layout; 2580 2581 PetscFunctionBegin; 2582 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 2583 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 2584 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 2585 if (size==1) PetscFunctionReturn(0); 2586 2587 ierr = PetscLogEventBegin(DMPLEX_RebalanceSharedPoints, dm, 0, 0, 0);CHKERRQ(ierr); 2588 2589 ierr = PetscOptionsGetViewer(comm,((PetscObject)dm)->options, prefix,"-dm_rebalance_partition_view",&viewer,&format,NULL);CHKERRQ(ierr); 2590 if(viewer) { 2591 ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr); 2592 } 2593 2594 /* Figure out all points in the plex that we are interested in balancing. */ 2595 ierr = DMPlexGetDepthStratum(dm, entityDepth, &eBegin, &eEnd);CHKERRQ(ierr); 2596 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2597 ierr = PetscMalloc1(pEnd-pStart, &toBalance);CHKERRQ(ierr); 2598 2599 for (i=0; i<pEnd-pStart; i++) { 2600 toBalance[i] = (i-pStart>=eBegin && i-pStart<eEnd); 2601 } 2602 2603 /* There are three types of points: 2604 * exclusivelyOwned: points that are owned by this process and only seen by this process 2605 * nonExclusivelyOwned: points that are owned by this process but seen by at least another process 2606 * leaf: a point that is seen by this process but owned by a different process 2607 */ 2608 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2609 ierr = PetscSFGetGraph(sf, &nroots, &nleafs, &ilocal, &iremote); CHKERRQ(ierr); 2610 ierr = PetscMalloc1(pEnd-pStart, &isLeaf);CHKERRQ(ierr); 2611 ierr = PetscMalloc1(pEnd-pStart, &isNonExclusivelyOwned);CHKERRQ(ierr); 2612 ierr = PetscMalloc1(pEnd-pStart, &isExclusivelyOwned);CHKERRQ(ierr); 2613 for (i=0; i<pEnd-pStart; i++) { 2614 isNonExclusivelyOwned[i] = PETSC_FALSE; 2615 isExclusivelyOwned[i] = PETSC_FALSE; 2616 isLeaf[i] = PETSC_FALSE; 2617 } 2618 2619 /* start by marking all the leafs */ 2620 for (i=0; i<nleafs; i++) { 2621 isLeaf[ilocal[i]-pStart] = PETSC_TRUE; 2622 } 2623 2624 /* for an owned point, we can figure out whether another processor sees it or 2625 * not by calculating its degree */ 2626 ierr = PetscSFComputeDegreeBegin(sf, °rees);CHKERRQ(ierr); 2627 ierr = PetscSFComputeDegreeEnd(sf, °rees);CHKERRQ(ierr); 2628 2629 numExclusivelyOwned=0; 2630 numNonExclusivelyOwned=0; 2631 for (i=0; i<pEnd-pStart; i++) { 2632 if (toBalance[i]) { 2633 if (degrees[i] > 0) { 2634 isNonExclusivelyOwned[i] = PETSC_TRUE; 2635 numNonExclusivelyOwned += 1; 2636 } else { 2637 if (!isLeaf[i]) { 2638 isExclusivelyOwned[i] = PETSC_TRUE; 2639 numExclusivelyOwned += 1; 2640 } 2641 } 2642 } 2643 } 2644 2645 /* We are going to build a graph with one vertex per core representing the 2646 * exclusively owned points and then one vertex per nonExclusively owned 2647 * point. */ 2648 2649 ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr); 2650 ierr = PetscLayoutSetLocalSize(layout, 1 + numNonExclusivelyOwned);CHKERRQ(ierr); 2651 ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr); 2652 ierr = PetscLayoutGetRanges(layout, &cumSumVertices);CHKERRQ(ierr); 2653 2654 ierr = PetscMalloc1(pEnd-pStart, &globalNumbersOfLocalOwnedVertices);CHKERRQ(ierr); 2655 offset = cumSumVertices[rank]; 2656 counter = 0; 2657 for (i=0; i<pEnd-pStart; i++) { 2658 if (toBalance[i]) { 2659 if (degrees[i] > 0) { 2660 globalNumbersOfLocalOwnedVertices[i] = counter + 1 + offset; 2661 counter++; 2662 } 2663 } 2664 } 2665 2666 /* send the global numbers of vertices I own to the leafs so that they know to connect to it */ 2667 ierr = PetscMalloc1(pEnd-pStart, &leafGlobalNumbers);CHKERRQ(ierr); 2668 ierr = PetscSFBcastBegin(sf, MPIU_INT, globalNumbersOfLocalOwnedVertices, leafGlobalNumbers);CHKERRQ(ierr); 2669 ierr = PetscSFBcastEnd(sf, MPIU_INT, globalNumbersOfLocalOwnedVertices, leafGlobalNumbers);CHKERRQ(ierr); 2670 2671 /* Now start building the data structur for ParMETIS */ 2672 /* vtxdist = cum_sum_vertices */ 2673 2674 ierr = MatCreate(comm, &Apre);CHKERRQ(ierr); 2675 ierr = MatSetType(Apre, MATPREALLOCATOR);CHKERRQ(ierr); 2676 ierr = MatSetSizes(Apre, 1+numNonExclusivelyOwned, 1+numNonExclusivelyOwned, cumSumVertices[size], cumSumVertices[size]);CHKERRQ(ierr); 2677 ierr = MatSetUp(Apre);CHKERRQ(ierr); 2678 2679 for (i=0; i<pEnd-pStart; i++) { 2680 if (toBalance[i]) { 2681 if (isNonExclusivelyOwned[i]) { 2682 ierr = MatSetValues(Apre, 1, &(cumSumVertices[rank]), 1, &(globalNumbersOfLocalOwnedVertices[i]), &one, INSERT_VALUES);CHKERRQ(ierr); 2683 ierr = MatSetValues(Apre, 1, &(globalNumbersOfLocalOwnedVertices[i]), 1, &(cumSumVertices[rank]), &one, INSERT_VALUES);CHKERRQ(ierr); 2684 } else if (isLeaf[i]) { 2685 ierr = MatSetValues(Apre, 1, &(cumSumVertices[rank]), 1, &(leafGlobalNumbers[i]), &one, INSERT_VALUES);CHKERRQ(ierr); 2686 ierr = MatSetValues(Apre, 1, &(leafGlobalNumbers[i]), 1, &(cumSumVertices[rank]), &one, INSERT_VALUES);CHKERRQ(ierr); 2687 } 2688 } 2689 } 2690 2691 ierr = MatAssemblyBegin(Apre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2692 ierr = MatAssemblyEnd(Apre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2693 2694 ierr = MatCreate(comm, &A);CHKERRQ(ierr); 2695 ierr = MatSetType(A, MATMPIAIJ);CHKERRQ(ierr); 2696 ierr = MatSetSizes(A, 1+numNonExclusivelyOwned, 1+numNonExclusivelyOwned, cumSumVertices[size], cumSumVertices[size]);CHKERRQ(ierr); 2697 ierr = MatPreallocatorPreallocate(Apre, PETSC_FALSE, A);CHKERRQ(ierr); 2698 ierr = MatDestroy(&Apre);CHKERRQ(ierr); 2699 2700 for (i=0; i<pEnd-pStart; i++) { 2701 if (toBalance[i]) { 2702 if (isNonExclusivelyOwned[i]) { 2703 ierr = MatSetValue(A, cumSumVertices[rank], globalNumbersOfLocalOwnedVertices[i], 1, INSERT_VALUES);CHKERRQ(ierr); 2704 ierr = MatSetValue(A, globalNumbersOfLocalOwnedVertices[i], cumSumVertices[rank], 1, INSERT_VALUES);CHKERRQ(ierr); 2705 } else if (isLeaf[i]) { 2706 ierr = MatSetValue(A, cumSumVertices[rank], leafGlobalNumbers[i], 1, INSERT_VALUES);CHKERRQ(ierr); 2707 ierr = MatSetValue(A, leafGlobalNumbers[i], cumSumVertices[rank], 1, INSERT_VALUES);CHKERRQ(ierr); 2708 } 2709 } 2710 } 2711 2712 ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2713 ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2714 ierr = PetscFree(leafGlobalNumbers);CHKERRQ(ierr); 2715 ierr = PetscFree(globalNumbersOfLocalOwnedVertices);CHKERRQ(ierr); 2716 2717 nparts = size; 2718 wgtflag = 2; 2719 numflag = 0; 2720 ncon = 2; 2721 real_t *tpwgts; 2722 ierr = PetscMalloc1(ncon * nparts, &tpwgts);CHKERRQ(ierr); 2723 for (i=0; i<ncon*nparts; i++) { 2724 tpwgts[i] = 1./(nparts); 2725 } 2726 2727 ierr = PetscMalloc1(ncon, &ubvec);CHKERRQ(ierr); 2728 ubvec[0] = 1.01; 2729 ubvec[1] = 1.01; 2730 lenadjncy = 0; 2731 for (i=0; i<1+numNonExclusivelyOwned; i++) { 2732 PetscInt temp=0; 2733 ierr = MatGetRow(A, cumSumVertices[rank] + i, &temp, NULL, NULL);CHKERRQ(ierr); 2734 lenadjncy += temp; 2735 ierr = MatRestoreRow(A, cumSumVertices[rank] + i, &temp, NULL, NULL);CHKERRQ(ierr); 2736 } 2737 ierr = PetscMalloc1(lenadjncy, &adjncy);CHKERRQ(ierr); 2738 lenxadj = 2 + numNonExclusivelyOwned; 2739 ierr = PetscMalloc1(lenxadj, &xadj);CHKERRQ(ierr); 2740 xadj[0] = 0; 2741 counter = 0; 2742 for (i=0; i<1+numNonExclusivelyOwned; i++) { 2743 PetscInt temp=0; 2744 const PetscInt *cols; 2745 ierr = MatGetRow(A, cumSumVertices[rank] + i, &temp, &cols, NULL);CHKERRQ(ierr); 2746 ierr = PetscMemcpy(&adjncy[counter], cols, temp*sizeof(PetscInt));CHKERRQ(ierr); 2747 counter += temp; 2748 xadj[i+1] = counter; 2749 ierr = MatRestoreRow(A, cumSumVertices[rank] + i, &temp, &cols, NULL);CHKERRQ(ierr); 2750 } 2751 2752 ierr = PetscMalloc1(cumSumVertices[rank+1]-cumSumVertices[rank], &part);CHKERRQ(ierr); 2753 ierr = PetscMalloc1(ncon*(1 + numNonExclusivelyOwned), &vtxwgt);CHKERRQ(ierr); 2754 vtxwgt[0] = numExclusivelyOwned; 2755 if (ncon>1) vtxwgt[1] = 1; 2756 for (i=0; i<numNonExclusivelyOwned; i++) { 2757 vtxwgt[ncon*(i+1)] = 1; 2758 if (ncon>1) vtxwgt[ncon*(i+1)+1] = 0; 2759 } 2760 2761 if (viewer) { 2762 ierr = PetscViewerASCIIPrintf(viewer, "Attempt rebalancing of shared points of depth %D on interface of mesh distribution.\n", entityDepth);CHKERRQ(ierr); 2763 ierr = PetscViewerASCIIPrintf(viewer, "Size of generated auxiliary graph: %D\n", cumSumVertices[size]);CHKERRQ(ierr); 2764 } 2765 if (parallel) { 2766 ierr = PetscMalloc1(4, &options);CHKERRQ(ierr); 2767 options[0] = 1; 2768 options[1] = 0; /* Verbosity */ 2769 options[2] = 0; /* Seed */ 2770 options[3] = PARMETIS_PSR_COUPLED; /* Seed */ 2771 if (viewer) { ierr = PetscViewerASCIIPrintf(viewer, "Using ParMETIS to partition graph.\n");CHKERRQ(ierr); } 2772 if (useInitialGuess) { 2773 if (viewer) { ierr = PetscViewerASCIIPrintf(viewer, "Using current distribution of points as initial guess.\n");CHKERRQ(ierr); } 2774 PetscStackPush("ParMETIS_V3_RefineKway"); 2775 ierr = ParMETIS_V3_RefineKway((PetscInt*)cumSumVertices, xadj, adjncy, vtxwgt, adjwgt, &wgtflag, &numflag, &ncon, &nparts, tpwgts, ubvec, options, &edgecut, part, &comm); 2776 PetscStackPop; 2777 } else { 2778 PetscStackPush("ParMETIS_V3_PartKway"); 2779 ierr = ParMETIS_V3_PartKway((PetscInt*)cumSumVertices, xadj, adjncy, vtxwgt, adjwgt, &wgtflag, &numflag, &ncon, &nparts, tpwgts, ubvec, options, &edgecut, part, &comm); 2780 PetscStackPop; 2781 } 2782 } else { 2783 if (viewer) { ierr = PetscViewerASCIIPrintf(viewer, "Using METIS to partition graph.\n");CHKERRQ(ierr); } 2784 Mat As; 2785 PetscInt numRows; 2786 PetscInt *partGlobal; 2787 ierr = MatCreateRedundantMatrix(A, size, MPI_COMM_NULL, MAT_INITIAL_MATRIX, &As);CHKERRQ(ierr); 2788 2789 PetscInt *numExclusivelyOwnedAll; 2790 ierr = PetscMalloc1(size, &numExclusivelyOwnedAll);CHKERRQ(ierr); 2791 numExclusivelyOwnedAll[rank] = numExclusivelyOwned; 2792 ierr = MPI_Allgather(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,numExclusivelyOwnedAll,1,MPIU_INT,comm);CHKERRQ(ierr); 2793 2794 ierr = MatGetSize(As, &numRows, NULL);CHKERRQ(ierr); 2795 ierr = PetscMalloc1(numRows, &partGlobal);CHKERRQ(ierr); 2796 if (!rank) { 2797 PetscInt *adjncy_g, *xadj_g, *vtxwgt_g; 2798 lenadjncy = 0; 2799 2800 for (i=0; i<numRows; i++) { 2801 PetscInt temp=0; 2802 ierr = MatGetRow(As, i, &temp, NULL, NULL);CHKERRQ(ierr); 2803 lenadjncy += temp; 2804 ierr = MatRestoreRow(As, i, &temp, NULL, NULL);CHKERRQ(ierr); 2805 } 2806 ierr = PetscMalloc1(lenadjncy, &adjncy_g);CHKERRQ(ierr); 2807 lenxadj = 1 + numRows; 2808 ierr = PetscMalloc1(lenxadj, &xadj_g);CHKERRQ(ierr); 2809 xadj_g[0] = 0; 2810 counter = 0; 2811 for (i=0; i<numRows; i++) { 2812 PetscInt temp=0; 2813 const PetscInt *cols; 2814 ierr = MatGetRow(As, i, &temp, &cols, NULL);CHKERRQ(ierr); 2815 ierr = PetscMemcpy(&adjncy_g[counter], cols, temp*sizeof(PetscInt));CHKERRQ(ierr); 2816 counter += temp; 2817 xadj_g[i+1] = counter; 2818 ierr = MatRestoreRow(As, i, &temp, &cols, NULL);CHKERRQ(ierr); 2819 } 2820 ierr = PetscMalloc1(2*numRows, &vtxwgt_g);CHKERRQ(ierr); 2821 for (i=0; i<size; i++){ 2822 vtxwgt_g[ncon*cumSumVertices[i]] = numExclusivelyOwnedAll[i]; 2823 if (ncon>1) vtxwgt_g[ncon*cumSumVertices[i]+1] = 1; 2824 for (j=cumSumVertices[i]+1; j<cumSumVertices[i+1]; j++) { 2825 vtxwgt_g[ncon*j] = 1; 2826 if (ncon>1) vtxwgt_g[2*j+1] = 0; 2827 } 2828 } 2829 ierr = PetscMalloc1(64, &options);CHKERRQ(ierr); 2830 ierr = METIS_SetDefaultOptions(options); /* initialize all defaults */ 2831 options[METIS_OPTION_CONTIG] = 1; 2832 PetscStackPush("METIS_PartGraphKway"); 2833 METIS_PartGraphKway(&numRows, &ncon, xadj_g, adjncy_g, vtxwgt_g, NULL, NULL, &nparts, tpwgts, ubvec, options, &edgecut, partGlobal); 2834 PetscStackPop; 2835 ierr = PetscFree(xadj_g);CHKERRQ(ierr); 2836 ierr = PetscFree(adjncy_g);CHKERRQ(ierr); 2837 ierr = PetscFree(vtxwgt_g);CHKERRQ(ierr); 2838 } 2839 ierr = PetscFree(numExclusivelyOwnedAll);CHKERRQ(ierr); 2840 2841 /* Now scatter the parts array. */ 2842 { 2843 PetscInt *counts; 2844 ierr = PetscMalloc1(size, &counts);CHKERRQ(ierr); 2845 for(i=0; i<size; i++) { 2846 counts[i] = cumSumVertices[i+1] - cumSumVertices[i]; 2847 } 2848 ierr = MPI_Scatterv(partGlobal, counts, cumSumVertices, MPIU_INT, part, counts[rank], MPIU_INT, 0, comm);CHKERRQ(ierr); 2849 ierr = PetscFree(counts);CHKERRQ(ierr); 2850 } 2851 2852 ierr = PetscFree(partGlobal);CHKERRQ(ierr); 2853 ierr = MatDestroy(&As);CHKERRQ(ierr); 2854 } 2855 2856 ierr = MatDestroy(&A);CHKERRQ(ierr); 2857 ierr = PetscFree(ubvec);CHKERRQ(ierr); 2858 ierr = PetscFree(tpwgts);CHKERRQ(ierr); 2859 ierr = PetscFree(options);CHKERRQ(ierr); 2860 2861 /* Now rename the result so that the vertex resembling the exclusively owned points stays on the same rank */ 2862 2863 ierr = PetscMalloc1(size, &firstVertices);CHKERRQ(ierr); 2864 ierr = PetscMalloc1(size, &renumbering);CHKERRQ(ierr); 2865 firstVertices[rank] = part[0]; 2866 ierr = MPI_Allgather(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,firstVertices,1,MPIU_INT,comm);CHKERRQ(ierr); 2867 for (i=0; i<size; i++) { 2868 renumbering[firstVertices[i]] = i; 2869 } 2870 for (i=0; i<cumSumVertices[rank+1]-cumSumVertices[rank]; i++) { 2871 part[i] = renumbering[part[i]]; 2872 } 2873 /* Check if the renumbering worked (this can fail when ParMETIS gives fewer partitions than there are processes) */ 2874 failed = (PetscInt)(part[0] != rank); 2875 ierr = MPI_Allreduce(&failed, &failedGlobal, 1, MPIU_INT, MPI_SUM, comm);CHKERRQ(ierr); 2876 2877 ierr = PetscFree(firstVertices);CHKERRQ(ierr); 2878 ierr = PetscFree(renumbering);CHKERRQ(ierr); 2879 2880 if (failedGlobal > 0) { 2881 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 2882 ierr = PetscFree(xadj);CHKERRQ(ierr); 2883 ierr = PetscFree(adjncy);CHKERRQ(ierr); 2884 ierr = PetscFree(vtxwgt);CHKERRQ(ierr); 2885 ierr = PetscFree(toBalance);CHKERRQ(ierr); 2886 ierr = PetscFree(isLeaf);CHKERRQ(ierr); 2887 ierr = PetscFree(isNonExclusivelyOwned);CHKERRQ(ierr); 2888 ierr = PetscFree(isExclusivelyOwned);CHKERRQ(ierr); 2889 ierr = PetscFree(part);CHKERRQ(ierr); 2890 if (viewer) { 2891 ierr = PetscViewerPopFormat(viewer); 2892 ierr = PetscViewerDestroy(&viewer); 2893 } 2894 ierr = PetscLogEventEnd(DMPLEX_RebalanceSharedPoints, dm, 0, 0, 0);CHKERRQ(ierr); 2895 PetscFunctionReturn(1); 2896 } 2897 2898 /*Let's check how well we did distributing points*/ 2899 if (viewer) { 2900 ierr = PetscViewerASCIIPrintf(viewer, "Comparing number of owned entities of depth %D on each process before rebalancing, after rebalancing, and after consistency checks.\n", entityDepth);CHKERRQ(ierr); 2901 ierr = PetscViewerASCIIPrintf(viewer, "Initial. ");CHKERRQ(ierr); 2902 ierr = DMPlexViewDistribution(comm, cumSumVertices[rank+1]-cumSumVertices[rank], ncon, vtxwgt, NULL, viewer);CHKERRQ(ierr); 2903 ierr = PetscViewerASCIIPrintf(viewer, "Rebalanced. ");CHKERRQ(ierr); 2904 ierr = DMPlexViewDistribution(comm, cumSumVertices[rank+1]-cumSumVertices[rank], ncon, vtxwgt, part, viewer);CHKERRQ(ierr); 2905 } 2906 2907 /* Now check that every vertex is owned by a process that it is actually connected to. */ 2908 for (i=1; i<=numNonExclusivelyOwned; i++) { 2909 PetscInt loc = 0; 2910 ierr = PetscFindInt(cumSumVertices[part[i]], xadj[i+1]-xadj[i], &adjncy[xadj[i]], &loc);CHKERRQ(ierr); 2911 /* If not, then just set the owner to the original owner (hopefully a rare event, it means that a vertex has been isolated) */ 2912 if (loc<0) { 2913 part[i] = rank; 2914 } 2915 } 2916 2917 /* Let's see how significant the influences of the previous fixing up step was.*/ 2918 if (viewer) { 2919 ierr = PetscViewerASCIIPrintf(viewer, "After. ");CHKERRQ(ierr); 2920 ierr = DMPlexViewDistribution(comm, cumSumVertices[rank+1]-cumSumVertices[rank], ncon, vtxwgt, part, viewer);CHKERRQ(ierr); 2921 } 2922 2923 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 2924 ierr = PetscFree(xadj);CHKERRQ(ierr); 2925 ierr = PetscFree(adjncy);CHKERRQ(ierr); 2926 ierr = PetscFree(vtxwgt);CHKERRQ(ierr); 2927 2928 /* Almost done, now rewrite the SF to reflect the new ownership. */ 2929 { 2930 PetscInt *pointsToRewrite; 2931 ierr = PetscMalloc1(numNonExclusivelyOwned, &pointsToRewrite); 2932 counter = 0; 2933 for(i=0; i<pEnd-pStart; i++) { 2934 if (toBalance[i]) { 2935 if (isNonExclusivelyOwned[i]) { 2936 pointsToRewrite[counter] = i + pStart; 2937 counter++; 2938 } 2939 } 2940 } 2941 ierr = DMPlexRewriteSF(dm, numNonExclusivelyOwned, pointsToRewrite, part+1, degrees);CHKERRQ(ierr); 2942 ierr = PetscFree(pointsToRewrite);CHKERRQ(ierr); 2943 } 2944 2945 ierr = PetscFree(toBalance);CHKERRQ(ierr); 2946 ierr = PetscFree(isLeaf);CHKERRQ(ierr); 2947 ierr = PetscFree(isNonExclusivelyOwned);CHKERRQ(ierr); 2948 ierr = PetscFree(isExclusivelyOwned);CHKERRQ(ierr); 2949 ierr = PetscFree(part);CHKERRQ(ierr); 2950 if (viewer) { 2951 ierr = PetscViewerPopFormat(viewer); 2952 ierr = PetscViewerDestroy(&viewer); 2953 } 2954 ierr = PetscLogEventEnd(DMPLEX_RebalanceSharedPoints, dm, 0, 0, 0);CHKERRQ(ierr); 2955 #else 2956 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Mesh partitioning needs external package support.\nPlease reconfigure with --download-parmetis."); 2957 #endif 2958 PetscFunctionReturn(0); 2959 } 2960