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 static PetscErrorCode DMPlexViewDistribution(MPI_Comm comm, PetscInt n, PetscInt skip, PetscInt *vtxwgt, PetscInt *part, PetscViewer viewer) 2356 { 2357 PetscInt *distribution, min, max, sum, size, rank, i, ierr; 2358 PetscFunctionBegin; 2359 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 2360 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 2361 ierr = PetscCalloc1(size, &distribution);CHKERRQ(ierr); 2362 for (i=0; i<n; i++) { 2363 if (part) distribution[part[i]] += vtxwgt[skip*i]; 2364 else distribution[rank] += vtxwgt[skip*i]; 2365 } 2366 ierr = MPI_Allreduce(MPI_IN_PLACE, distribution, size, MPIU_INT, MPI_SUM, comm);CHKERRQ(ierr); 2367 min = distribution[0]; 2368 max = distribution[0]; 2369 sum = distribution[0]; 2370 for (i=1; i<size; i++) { 2371 if (distribution[i]<min) min=distribution[i]; 2372 if (distribution[i]>max) max=distribution[i]; 2373 sum += distribution[i]; 2374 } 2375 ierr = PetscViewerASCIIPrintf(viewer, "Min: %D, Avg: %D, Max: %D, Balance: %f\n", min, sum/size, max, (max*1.*size)/sum);CHKERRQ(ierr); 2376 ierr = PetscFree(distribution);CHKERRQ(ierr); 2377 PetscFunctionReturn(0); 2378 } 2379 2380 /*@ 2381 DMPlexRebalanceSharedPoints - Redistribute points in the plex that are shared in order to achieve better balancing. This routine updates the PointSF of the DM inplace. 2382 2383 Input parameters: 2384 + dm - The DMPlex object. 2385 + entityDepth: depth of the entity to balance (0 -> balance vertices). 2386 + useInitialGuess: whether to use the current distribution as initial guess (only used by ParMETIS). 2387 + parallel: Whether to use ParMETIS and do the partition in parallel or whether to gather the graph onto a single process and use METIS. 2388 2389 Level: user 2390 2391 @*/ 2392 2393 PetscErrorCode DMPlexRebalanceSharedPoints(DM dm, PetscInt entityDepth, PetscBool useInitialGuess, PetscBool parallel) 2394 { 2395 #if defined(PETSC_HAVE_PARMETIS) 2396 PetscSF sf; 2397 PetscInt ierr, i, j; 2398 PetscInt eBegin, eEnd, nroots, nleafs, pStart, pEnd, sumDegrees; 2399 const PetscInt *degree, *ilocal; 2400 const PetscSFNode *iremote; /* Do I need to free these? */ 2401 PetscBool *toBalance, *isLeaf, *isExclusivelyOwned, *isNonExclusivelyOwned; 2402 PetscInt numExclusivelyOwned, numNonExclusivelyOwned; 2403 PetscMPIInt rank, size; 2404 PetscInt *cumSumDegrees, *globalNumbersOfLocalOwnedVertices, *locationsOfLeafs, *rankOnLeafs, *remoteLocalPointOfLeafs, *points, *leafGlobalNumbers; 2405 const PetscInt *cumSumVertices; 2406 PetscInt offset, counter; 2407 PetscInt lenadjncy, numNonExclusivelyOwnedConnectTo, numLeafs; 2408 PetscInt *xadj, *adjncy, *vtxwgt; 2409 PetscInt lenxadj; 2410 2411 PetscInt *adjwgt = NULL; 2412 PetscInt *part, *options; 2413 PetscInt nparts, wgtflag, numflag, ncon, edgecut; 2414 real_t *ubvec; 2415 PetscInt *firstVertices, *renumbering; 2416 PetscInt failed, failedGlobal; 2417 MPI_Comm comm; 2418 PetscInt leafCounter; 2419 PetscInt *leafsNew; 2420 PetscSFNode *leafLocationsNew; 2421 Mat A, Apre; 2422 PetscScalar one = 1; 2423 const char *prefix = NULL; 2424 PetscViewer viewer; 2425 PetscViewerFormat format; 2426 2427 PetscFunctionBegin; 2428 2429 ierr = PetscLogEventBegin(DMPLEX_RebalanceSharedPoints, dm, 0, 0, 0);CHKERRQ(ierr); 2430 2431 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 2432 2433 ierr = PetscOptionsGetViewer(comm,((PetscObject)dm)->options, prefix,"-dm_rebalance_partition_view",&viewer,&format,NULL); 2434 if(viewer) { 2435 ierr = PetscViewerPushFormat(viewer,format); 2436 } 2437 2438 2439 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 2440 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 2441 if (size==1) PetscFunctionReturn(0); 2442 2443 /* Figure out all points in the plex that we are interested in balancing. */ 2444 ierr = DMPlexGetDepthStratum(dm, entityDepth, &eBegin, &eEnd);CHKERRQ(ierr); 2445 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2446 ierr = PetscMalloc1(pEnd-pStart, &toBalance);CHKERRQ(ierr); 2447 2448 for (i=0; i<pEnd-pStart; i++) { 2449 toBalance[i] = (i-pStart>=eBegin && i-pStart<eEnd); 2450 } 2451 2452 2453 /* There are three types of points: 2454 * exclusivelyOwned: points that are owned by this process and only seen by this process 2455 * nonExclusivelyOwned: points that are owned by this process but seen by at least another process 2456 * leaf: a point that is seen by this process but owned by a different process 2457 */ 2458 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2459 ierr = PetscSFGetGraph(sf, &nroots, &nleafs, &ilocal, &iremote); CHKERRQ(ierr); 2460 ierr = PetscMalloc1(pEnd-pStart, &isLeaf);CHKERRQ(ierr); 2461 ierr = PetscMalloc1(pEnd-pStart, &isNonExclusivelyOwned);CHKERRQ(ierr); 2462 ierr = PetscMalloc1(pEnd-pStart, &isExclusivelyOwned);CHKERRQ(ierr); 2463 for (i=0; i<pEnd-pStart; i++) { 2464 isNonExclusivelyOwned[i] = PETSC_FALSE; 2465 isExclusivelyOwned[i] = PETSC_FALSE; 2466 isLeaf[i] = PETSC_FALSE; 2467 } 2468 2469 2470 /* start by marking all the leafs */ 2471 for (i=0; i<nleafs; i++) { 2472 isLeaf[ilocal[i]-pStart] = PETSC_TRUE; 2473 } 2474 2475 /* for an owned point, we can figure out whether another processor sees it or 2476 * not by calculating its degree */ 2477 ierr = PetscSFComputeDegreeBegin(sf, °ree);CHKERRQ(ierr); 2478 ierr = PetscSFComputeDegreeEnd(sf, °ree);CHKERRQ(ierr); 2479 2480 numExclusivelyOwned=0; 2481 numNonExclusivelyOwned=0; 2482 for (i=0; i<pEnd-pStart; i++) { 2483 if (toBalance[i]) { 2484 if (degree[i] > 0) { 2485 isNonExclusivelyOwned[i] = PETSC_TRUE; 2486 numNonExclusivelyOwned += 1; 2487 } else { 2488 if (!isLeaf[i]) { 2489 isExclusivelyOwned[i] = PETSC_TRUE; 2490 numExclusivelyOwned += 1; 2491 } 2492 } 2493 } 2494 } 2495 2496 2497 /* We are going to build a graph with one vertex per core representing the 2498 * exclusively owned points and then one vertex per nonExclusively owned 2499 * point. */ 2500 2501 PetscLayout layout; 2502 ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr); 2503 ierr = PetscLayoutSetLocalSize(layout, 1 + numNonExclusivelyOwned);CHKERRQ(ierr); 2504 ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr); 2505 ierr = PetscLayoutGetRanges(layout, &cumSumVertices);CHKERRQ(ierr); 2506 2507 ierr = PetscMalloc1(pEnd-pStart+1, &cumSumDegrees);CHKERRQ(ierr); 2508 cumSumDegrees[0] = 0; 2509 for (i=1; i<=pEnd-pStart; i++) { 2510 cumSumDegrees[i] = cumSumDegrees[i-1] + degree[i-1]; 2511 } 2512 ierr = PetscMalloc1(pEnd-pStart, &globalNumbersOfLocalOwnedVertices);CHKERRQ(ierr); 2513 2514 offset = cumSumVertices[rank]; 2515 counter = 0; 2516 for (i=0; i<pEnd-pStart; i++) { 2517 if (toBalance[i]) { 2518 if (degree[i] > 0) { 2519 globalNumbersOfLocalOwnedVertices[i] = counter + 1 + offset; 2520 counter++; 2521 } 2522 } 2523 } 2524 2525 /* get the location of my leafs (we have sumDegrees many leafs pointing at our roots) */ 2526 sumDegrees = 0; 2527 for (i=0; i<pEnd-pStart; i++) { 2528 sumDegrees += degree[i]; 2529 } 2530 2531 ierr = PetscMalloc1(sumDegrees, &locationsOfLeafs);CHKERRQ(ierr); 2532 ierr = PetscMalloc1(pEnd-pStart, &rankOnLeafs);CHKERRQ(ierr); 2533 for (i=0; i<pEnd-pStart; i++) { 2534 rankOnLeafs[i] = rank; 2535 } 2536 ierr = PetscSFGatherBegin(sf, MPIU_INT, rankOnLeafs, locationsOfLeafs);CHKERRQ(ierr); 2537 ierr = PetscSFGatherEnd(sf, MPIU_INT, rankOnLeafs, locationsOfLeafs);CHKERRQ(ierr); 2538 ierr = PetscFree(rankOnLeafs);CHKERRQ(ierr); 2539 2540 /* get the remote local points of my leaves */ 2541 ierr = PetscMalloc1(sumDegrees, &remoteLocalPointOfLeafs);CHKERRQ(ierr); 2542 ierr = PetscMalloc1(pEnd-pStart, &points);CHKERRQ(ierr); 2543 for (i=0; i<pEnd-pStart; i++) { 2544 points[i] = pStart+i; 2545 } 2546 ierr = PetscSFGatherBegin(sf, MPIU_INT, points, remoteLocalPointOfLeafs);CHKERRQ(ierr); 2547 ierr = PetscSFGatherEnd(sf, MPIU_INT, points, remoteLocalPointOfLeafs);CHKERRQ(ierr); 2548 ierr = PetscFree(points);CHKERRQ(ierr); 2549 2550 /* send the global numbers of vertices I own to the leafs so that they know to connect to it */ 2551 ierr = PetscMalloc1(pEnd-pStart, &leafGlobalNumbers);CHKERRQ(ierr); 2552 ierr = PetscSFBcastBegin(sf, MPIU_INT, globalNumbersOfLocalOwnedVertices, leafGlobalNumbers);CHKERRQ(ierr); 2553 ierr = PetscSFBcastEnd(sf, MPIU_INT, globalNumbersOfLocalOwnedVertices, leafGlobalNumbers);CHKERRQ(ierr); 2554 2555 /* Now start building the data structur for ParMETIS */ 2556 /* vtxdist = cum_sum_vertices */ 2557 2558 numNonExclusivelyOwnedConnectTo = 0; 2559 numLeafs = 0; 2560 for (i=0; i<pEnd-pStart; i++) { 2561 if (toBalance[i]) { 2562 if (isNonExclusivelyOwned[i]) { 2563 numNonExclusivelyOwnedConnectTo += 1 + degree[i]; 2564 } 2565 if (isLeaf[i]) { 2566 numLeafs++; 2567 } 2568 } 2569 } 2570 2571 2572 ierr = MatCreate(comm, &Apre);CHKERRQ(ierr); 2573 ierr = MatSetType(Apre, MATPREALLOCATOR);CHKERRQ(ierr); 2574 ierr = MatSetSizes(Apre, 1+numNonExclusivelyOwned, 1+numNonExclusivelyOwned, cumSumVertices[size], cumSumVertices[size]);CHKERRQ(ierr); 2575 ierr = MatSetUp(Apre);CHKERRQ(ierr); 2576 2577 for (i=0; i<pEnd-pStart; i++) { 2578 if (toBalance[i]) { 2579 if (isNonExclusivelyOwned[i]) { 2580 ierr = MatSetValues(Apre, 1, &(cumSumVertices[rank]), 1, &(globalNumbersOfLocalOwnedVertices[i]), &one, INSERT_VALUES);CHKERRQ(ierr); 2581 ierr = MatSetValues(Apre, 1, &(globalNumbersOfLocalOwnedVertices[i]), 1, &(cumSumVertices[rank]), &one, INSERT_VALUES);CHKERRQ(ierr); 2582 } else if (isLeaf[i]) { 2583 ierr = MatSetValues(Apre, 1, &(cumSumVertices[rank]), 1, &(leafGlobalNumbers[i]), &one, INSERT_VALUES);CHKERRQ(ierr); 2584 ierr = MatSetValues(Apre, 1, &(leafGlobalNumbers[i]), 1, &(cumSumVertices[rank]), &one, INSERT_VALUES);CHKERRQ(ierr); 2585 } 2586 } 2587 } 2588 2589 ierr = MatAssemblyBegin(Apre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2590 ierr = MatAssemblyEnd(Apre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2591 2592 ierr = MatCreate(comm, &A);CHKERRQ(ierr); 2593 ierr = MatSetType(A, MATMPIAIJ);CHKERRQ(ierr); 2594 ierr = MatSetSizes(A, 1+numNonExclusivelyOwned, 1+numNonExclusivelyOwned, cumSumVertices[size], cumSumVertices[size]);CHKERRQ(ierr); 2595 ierr = MatPreallocatorPreallocate(Apre, PETSC_FALSE, A);CHKERRQ(ierr); 2596 ierr = MatDestroy(&Apre);CHKERRQ(ierr); 2597 2598 for (i=0; i<pEnd-pStart; i++) { 2599 if (toBalance[i]) { 2600 if (isNonExclusivelyOwned[i]) { 2601 ierr = MatSetValue(A, cumSumVertices[rank], globalNumbersOfLocalOwnedVertices[i], 1, INSERT_VALUES);CHKERRQ(ierr); 2602 ierr = MatSetValue(A, globalNumbersOfLocalOwnedVertices[i], cumSumVertices[rank], 1, INSERT_VALUES);CHKERRQ(ierr); 2603 } else if (isLeaf[i]) { 2604 ierr = MatSetValue(A, cumSumVertices[rank], leafGlobalNumbers[i], 1, INSERT_VALUES);CHKERRQ(ierr); 2605 ierr = MatSetValue(A, leafGlobalNumbers[i], cumSumVertices[rank], 1, INSERT_VALUES);CHKERRQ(ierr); 2606 } 2607 } 2608 } 2609 2610 ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2611 ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2612 ierr = PetscFree(leafGlobalNumbers);CHKERRQ(ierr); 2613 ierr = PetscFree(globalNumbersOfLocalOwnedVertices);CHKERRQ(ierr); 2614 2615 nparts = size; 2616 wgtflag = 2; 2617 2618 numflag = 0; 2619 ncon = 2; 2620 real_t *tpwgts; 2621 ierr = PetscMalloc1(ncon * nparts, &tpwgts);CHKERRQ(ierr); 2622 2623 for (i=0; i<ncon*nparts; i++) { 2624 tpwgts[i] = 1./(nparts); 2625 } 2626 2627 2628 ierr = PetscMalloc1(ncon, &ubvec);CHKERRQ(ierr); 2629 ubvec[0] = 1.01; 2630 if (ncon>1) ubvec[1] = 1.01; 2631 ierr = PetscMalloc1(1, &options);CHKERRQ(ierr); 2632 options[0] = 0; 2633 lenadjncy = 0; 2634 for (i=0; i<1+numNonExclusivelyOwned; i++) { 2635 PetscInt temp=0; 2636 ierr = MatGetRow(A, cumSumVertices[rank] + i, &temp, NULL, NULL);CHKERRQ(ierr); 2637 lenadjncy += temp; 2638 ierr = MatRestoreRow(A, cumSumVertices[rank] + i, &temp, NULL, NULL);CHKERRQ(ierr); 2639 } 2640 ierr = PetscMalloc1(lenadjncy, &adjncy);CHKERRQ(ierr); 2641 lenxadj = 2 + numNonExclusivelyOwned; 2642 ierr = PetscMalloc1(lenxadj, &xadj);CHKERRQ(ierr); 2643 xadj[0] = 0; 2644 counter = 0; 2645 for (i=0; i<1+numNonExclusivelyOwned; i++) { 2646 PetscInt temp=0; 2647 const PetscInt *cols; 2648 ierr = MatGetRow(A, cumSumVertices[rank] + i, &temp, &cols, NULL);CHKERRQ(ierr); 2649 ierr = PetscMemcpy(&adjncy[counter], cols, temp*sizeof(PetscInt));CHKERRQ(ierr); 2650 counter += temp; 2651 xadj[i+1] = counter; 2652 ierr = MatRestoreRow(A, cumSumVertices[rank] + i, &temp, &cols, NULL);CHKERRQ(ierr); 2653 } 2654 2655 2656 ierr = PetscMalloc1(cumSumVertices[rank+1]-cumSumVertices[rank], &part);CHKERRQ(ierr); 2657 ierr = PetscMalloc1(ncon*(1 + numNonExclusivelyOwned), &vtxwgt);CHKERRQ(ierr); 2658 vtxwgt[0] = numExclusivelyOwned; 2659 if (ncon>1) vtxwgt[1] = 1; 2660 for (i=0; i<numNonExclusivelyOwned; i++) { 2661 vtxwgt[ncon*(i+1)] = 1; 2662 if (ncon>1) vtxwgt[ncon*(i+1)+1] = 0; 2663 } 2664 2665 if (viewer) { 2666 ierr = PetscViewerASCIIPrintf(viewer, "Attempt rebalancing of shared points of depth %D on interface of mesh distribution.\n", entityDepth);CHKERRQ(ierr); 2667 ierr = PetscViewerASCIIPrintf(viewer, "Size of generated auxiliary graph: %D\n", cumSumVertices[size]);CHKERRQ(ierr); 2668 } 2669 if (parallel) { 2670 if (viewer) { ierr = PetscViewerASCIIPrintf(viewer, "Using ParMETIS to partition graph.\n");CHKERRQ(ierr); } 2671 if (useInitialGuess) { 2672 if (viewer) { ierr = PetscViewerASCIIPrintf(viewer, "Using current distribution of points as initial guess.\n");CHKERRQ(ierr); } 2673 PetscStackPush("ParMETIS_V3_RefineKway"); 2674 ierr = ParMETIS_V3_RefineKway((PetscInt*)cumSumVertices, xadj, adjncy, vtxwgt, adjwgt, &wgtflag, &numflag, &ncon, &nparts, tpwgts, ubvec, options, &edgecut, part, &comm); 2675 PetscStackPop; 2676 } else { 2677 PetscStackPush("ParMETIS_V3_PartKway"); 2678 ierr = ParMETIS_V3_PartKway((PetscInt*)cumSumVertices, xadj, adjncy, vtxwgt, adjwgt, &wgtflag, &numflag, &ncon, &nparts, tpwgts, ubvec, options, &edgecut, part, &comm); 2679 PetscStackPop; 2680 } 2681 } else { 2682 if (viewer) { ierr = PetscViewerASCIIPrintf(viewer, "Using METIS to partition graph.\n");CHKERRQ(ierr); } 2683 Mat As; 2684 PetscInt numRows; 2685 PetscInt *partGlobal; 2686 ierr = MatCreateRedundantMatrix(A, size, MPI_COMM_NULL, MAT_INITIAL_MATRIX, &As);CHKERRQ(ierr); 2687 2688 PetscInt *numExclusivelyOwnedAll; 2689 ierr = PetscMalloc1(size, &numExclusivelyOwnedAll);CHKERRQ(ierr); 2690 numExclusivelyOwnedAll[rank] = numExclusivelyOwned; 2691 ierr = MPI_Allgather(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,numExclusivelyOwnedAll,1,MPIU_INT,comm);CHKERRQ(ierr); 2692 2693 ierr = MatGetSize(As, &numRows, NULL);CHKERRQ(ierr); 2694 ierr = PetscMalloc1(numRows, &partGlobal);CHKERRQ(ierr); 2695 if (!rank) { 2696 PetscInt *adjncy_g, *xadj_g, *vtxwgt_g; 2697 lenadjncy = 0; 2698 2699 for (i=0; i<numRows; i++) { 2700 PetscInt temp=0; 2701 ierr = MatGetRow(As, i, &temp, NULL, NULL);CHKERRQ(ierr); 2702 lenadjncy += temp; 2703 ierr = MatRestoreRow(As, i, &temp, NULL, NULL);CHKERRQ(ierr); 2704 } 2705 ierr = PetscMalloc1(lenadjncy, &adjncy_g);CHKERRQ(ierr); 2706 lenxadj = 1 + numRows; 2707 ierr = PetscMalloc1(lenxadj, &xadj_g);CHKERRQ(ierr); 2708 xadj_g[0] = 0; 2709 counter = 0; 2710 for (i=0; i<numRows; i++) { 2711 PetscInt temp=0; 2712 const PetscInt *cols; 2713 ierr = MatGetRow(As, i, &temp, &cols, NULL);CHKERRQ(ierr); 2714 ierr = PetscMemcpy(&adjncy_g[counter], cols, temp*sizeof(PetscInt));CHKERRQ(ierr); 2715 counter += temp; 2716 xadj_g[i+1] = counter; 2717 ierr = MatRestoreRow(As, i, &temp, &cols, NULL);CHKERRQ(ierr); 2718 } 2719 ierr = PetscMalloc1(2*numRows, &vtxwgt_g);CHKERRQ(ierr); 2720 for (i=0; i<size; i++){ 2721 vtxwgt_g[ncon*cumSumVertices[i]] = numExclusivelyOwnedAll[i]; 2722 if (ncon>1) vtxwgt_g[ncon*cumSumVertices[i]+1] = 1; 2723 for (j=cumSumVertices[i]+1; j<cumSumVertices[i+1]; j++) { 2724 vtxwgt_g[ncon*j] = 1; 2725 if (ncon>1) vtxwgt_g[2*j+1] = 0; 2726 } 2727 } 2728 ierr = PetscMalloc1(64, &options);CHKERRQ(ierr); 2729 ierr = METIS_SetDefaultOptions(options); /* initialize all defaults */ 2730 options[METIS_OPTION_CONTIG] = 1; 2731 PetscStackPush("METIS_PartGraphKway"); 2732 METIS_PartGraphKway(&numRows, &ncon, xadj_g, adjncy_g, vtxwgt_g, NULL, NULL, &nparts, tpwgts, ubvec, options, &edgecut, partGlobal); 2733 PetscStackPop; 2734 ierr = PetscFree(xadj_g);CHKERRQ(ierr); 2735 ierr = PetscFree(adjncy_g);CHKERRQ(ierr); 2736 ierr = PetscFree(vtxwgt_g);CHKERRQ(ierr); 2737 } 2738 ierr = PetscFree(numExclusivelyOwnedAll);CHKERRQ(ierr); 2739 2740 /* Now scatter the parts array. */ 2741 { 2742 PetscInt *counts; 2743 ierr = PetscMalloc1(size, &counts);CHKERRQ(ierr); 2744 for(i=0; i<size; i++) { 2745 counts[i] = cumSumVertices[i+1] - cumSumVertices[i]; 2746 } 2747 ierr = MPI_Scatterv(partGlobal, counts, cumSumVertices, MPIU_INT, part, counts[rank], MPIU_INT, 0, comm);CHKERRQ(ierr); 2748 ierr = PetscFree(counts);CHKERRQ(ierr); 2749 } 2750 2751 ierr = PetscFree(partGlobal);CHKERRQ(ierr); 2752 ierr = MatDestroy(&As);CHKERRQ(ierr); 2753 } 2754 2755 ierr = MatDestroy(&A);CHKERRQ(ierr); 2756 ierr = PetscFree(ubvec);CHKERRQ(ierr); 2757 ierr = PetscFree(tpwgts);CHKERRQ(ierr); 2758 ierr = PetscFree(options);CHKERRQ(ierr); 2759 2760 2761 /* Now rename the result so that the vertex resembling the exclusively owned points stays on the same rank */ 2762 2763 ierr = PetscMalloc1(size, &firstVertices);CHKERRQ(ierr); 2764 ierr = PetscMalloc1(size, &renumbering);CHKERRQ(ierr); 2765 firstVertices[rank] = part[0]; 2766 ierr = MPI_Allgather(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,firstVertices,1,MPIU_INT,comm);CHKERRQ(ierr); 2767 for (i=0; i<size; i++) { 2768 renumbering[firstVertices[i]] = i; 2769 } 2770 for (i=0; i<cumSumVertices[rank+1]-cumSumVertices[rank]; i++) { 2771 part[i] = renumbering[part[i]]; 2772 } 2773 /* Check if the renumbering worked (this can fail when ParMETIS gives fewer partitions than there are processes) */ 2774 failed = (PetscInt)(part[0] != rank); 2775 ierr = MPI_Allreduce(&failed, &failedGlobal, 1, MPIU_INT, MPI_SUM, comm);CHKERRQ(ierr); 2776 2777 if (failedGlobal > 0) { 2778 PetscFunctionReturn(1); 2779 } 2780 2781 2782 /*Let's check how well we did distributing points*/ 2783 if (viewer) { 2784 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); 2785 ierr = PetscViewerASCIIPrintf(viewer, "Initial. ");CHKERRQ(ierr); 2786 ierr = DMPlexViewDistribution(comm, cumSumVertices[rank+1]-cumSumVertices[rank], ncon, vtxwgt, NULL, viewer);CHKERRQ(ierr); 2787 ierr = PetscViewerASCIIPrintf(viewer, "Rebalanced. ");CHKERRQ(ierr); 2788 ierr = DMPlexViewDistribution(comm, cumSumVertices[rank+1]-cumSumVertices[rank], ncon, vtxwgt, part, viewer);CHKERRQ(ierr); 2789 } 2790 2791 /* Now check that every vertex is owned by a process that it is actually connected to. */ 2792 for (i=1; i<=numNonExclusivelyOwned; i++) { 2793 PetscInt loc = 0; 2794 ierr = PetscFindInt(cumSumVertices[part[i]], xadj[i+1]-xadj[i], &adjncy[xadj[i]], &loc);CHKERRQ(ierr); 2795 /* If not, then just set the owner to the original owner (hopefully a rare event, it means that a vertex has been isolated) */ 2796 if (loc<0) { 2797 part[i] = rank; 2798 } 2799 } 2800 2801 /* Let's see how significant the influences of the previous fixing up step was.*/ 2802 if (viewer) { 2803 ierr = PetscViewerASCIIPrintf(viewer, "After. ");CHKERRQ(ierr); 2804 ierr = DMPlexViewDistribution(comm, cumSumVertices[rank+1]-cumSumVertices[rank], ncon, vtxwgt, part, viewer);CHKERRQ(ierr); 2805 } 2806 2807 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 2808 ierr = PetscFree(firstVertices);CHKERRQ(ierr); 2809 ierr = PetscFree(renumbering);CHKERRQ(ierr); 2810 ierr = PetscFree(xadj);CHKERRQ(ierr); 2811 ierr = PetscFree(adjncy);CHKERRQ(ierr); 2812 ierr = PetscFree(vtxwgt);CHKERRQ(ierr); 2813 2814 2815 /* Figure out the new owners of the vertices that are up for grabs and their numbers on the new owners */ 2816 PetscInt *newOwners, *newNumbers; 2817 ierr = PetscMalloc1(pEnd-pStart, &newOwners);CHKERRQ(ierr); 2818 ierr = PetscMalloc1(pEnd-pStart, &newNumbers);CHKERRQ(ierr); 2819 for (i=0; i<pEnd-pStart; i++) { 2820 newOwners[i] = -1; 2821 newNumbers[i] = -1; 2822 } 2823 { 2824 PetscInt oldNumber, newNumber, oldOwner, newOwner; 2825 counter = 1; 2826 for (i=0; i<pEnd-pStart; i++) { 2827 if (toBalance[i]) { 2828 if (isNonExclusivelyOwned[i]) { 2829 oldNumber = i; 2830 newNumber = -1; 2831 oldOwner = rank; 2832 newOwner = part[counter]; 2833 if (oldOwner == newOwner) { 2834 newNumber = oldNumber; 2835 } else { 2836 for (j=0; j<degree[i]; j++) { 2837 if (locationsOfLeafs[cumSumDegrees[oldNumber]+j] == newOwner) { 2838 newNumber = remoteLocalPointOfLeafs[cumSumDegrees[oldNumber]+j]; 2839 break; 2840 } 2841 } 2842 } 2843 if (newNumber == -1) SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_SUP, "Couldn't find the new owner of vertex."); 2844 2845 newOwners[oldNumber] = newOwner; 2846 newNumbers[oldNumber] = newNumber; 2847 counter++; 2848 } 2849 } 2850 } 2851 } 2852 ierr = PetscFree(cumSumDegrees);CHKERRQ(ierr); 2853 ierr = PetscFree(locationsOfLeafs);CHKERRQ(ierr); 2854 ierr = PetscFree(remoteLocalPointOfLeafs);CHKERRQ(ierr); 2855 2856 ierr = PetscSFBcastBegin(sf, MPIU_INT, newOwners, newOwners);CHKERRQ(ierr); 2857 ierr = PetscSFBcastEnd(sf, MPIU_INT, newOwners, newOwners);CHKERRQ(ierr); 2858 ierr = PetscSFBcastBegin(sf, MPIU_INT, newNumbers, newNumbers);CHKERRQ(ierr); 2859 ierr = PetscSFBcastEnd(sf, MPIU_INT, newNumbers, newNumbers);CHKERRQ(ierr); 2860 2861 /* Now count how many leafs we have on each processor. */ 2862 leafCounter=0; 2863 for (i=0; i<pEnd-pStart; i++) { 2864 if (toBalance[i]){ 2865 if (newOwners[i] >= 0 && newOwners[i] != rank) { 2866 leafCounter++; 2867 } 2868 } else { 2869 if (isLeaf[i]) { 2870 leafCounter++; 2871 } 2872 } 2873 } 2874 2875 /* Now set up the new sf by creating the leaf arrays */ 2876 ierr = PetscMalloc1(leafCounter, &leafsNew);CHKERRQ(ierr); 2877 ierr = PetscMalloc1(leafCounter, &leafLocationsNew);CHKERRQ(ierr); 2878 2879 counter = 0; 2880 leafCounter = 0; 2881 for (i=0; i<pEnd-pStart; i++) { 2882 if (toBalance[i]){ 2883 if (isLeaf[i]) { 2884 counter++; 2885 } 2886 if (newOwners[i] >= 0 && newOwners[i] != rank) { 2887 leafsNew[leafCounter] = i; 2888 leafLocationsNew[leafCounter].rank = newOwners[i]; 2889 leafLocationsNew[leafCounter].index = newNumbers[i]; 2890 leafCounter++; 2891 } 2892 } else { 2893 if (isLeaf[i]) { 2894 leafsNew[leafCounter] = i; 2895 leafLocationsNew[leafCounter].rank = iremote[counter].rank; 2896 leafLocationsNew[leafCounter].index = iremote[counter].index; 2897 leafCounter++; 2898 counter++; 2899 } 2900 } 2901 } 2902 2903 ierr = PetscSFSetGraph(sf, nroots, leafCounter, leafsNew, PETSC_OWN_POINTER, leafLocationsNew, PETSC_OWN_POINTER);CHKERRQ(ierr); 2904 2905 2906 ierr = PetscFree(toBalance);CHKERRQ(ierr); 2907 ierr = PetscFree(isLeaf);CHKERRQ(ierr); 2908 ierr = PetscFree(isNonExclusivelyOwned);CHKERRQ(ierr); 2909 ierr = PetscFree(isExclusivelyOwned);CHKERRQ(ierr); 2910 ierr = PetscFree(newOwners);CHKERRQ(ierr); 2911 ierr = PetscFree(newNumbers);CHKERRQ(ierr); 2912 if (viewer) { 2913 ierr = PetscViewerPopFormat(viewer); 2914 ierr = PetscViewerDestroy(&viewer); 2915 } 2916 ierr = PetscLogEventEnd(DMPLEX_RebalanceSharedPoints, dm, 0, 0, 0);CHKERRQ(ierr); 2917 #else 2918 SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_SUP, "Mesh partitioning needs external package support.\nPlease reconfigure with --download-parmetis."); 2919 #endif 2920 PetscFunctionReturn(0); 2921 } 2922