1 #include <petsc/private/sfimpl.h> /*I "petscsf.h" I*/ 2 #include <petsc/private/hashseti.h> 3 #include <petscctable.h> 4 5 #if defined(PETSC_USE_DEBUG) 6 # define PetscSFCheckGraphSet(sf,arg) do { \ 7 if (PetscUnlikely(!(sf)->graphset)) \ 8 SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call PetscSFSetGraph() or PetscSFSetGraphWithPattern() on argument %D \"%s\" before %s()",(arg),#sf,PETSC_FUNCTION_NAME); \ 9 } while (0) 10 #else 11 # define PetscSFCheckGraphSet(sf,arg) do {} while (0) 12 #endif 13 14 const char *const PetscSFDuplicateOptions[] = {"CONFONLY","RANKS","GRAPH","PetscSFDuplicateOption","PETSCSF_DUPLICATE_",0}; 15 16 /*@ 17 PetscSFCreate - create a star forest communication context 18 19 Collective 20 21 Input Arguments: 22 . comm - communicator on which the star forest will operate 23 24 Output Arguments: 25 . sf - new star forest context 26 27 Options Database Keys: 28 + -sf_type basic -Use MPI persistent Isend/Irecv for communication (Default) 29 . -sf_type window -Use MPI-3 one-sided window for communication 30 - -sf_type neighbor -Use MPI-3 neighborhood collectives for communication 31 32 Level: intermediate 33 34 Notes: 35 When one knows the communication graph is one of the predefined graph, such as MPI_Alltoall, MPI_Allgatherv, 36 MPI_Gatherv, one can create a PetscSF and then set its graph with PetscSFSetGraphWithPattern(). These special 37 SFs are optimized and they have better performance than general SFs. 38 39 .seealso: PetscSFSetGraph(), PetscSFSetGraphWithPattern(), PetscSFDestroy() 40 @*/ 41 PetscErrorCode PetscSFCreate(MPI_Comm comm,PetscSF *sf) 42 { 43 PetscErrorCode ierr; 44 PetscSF b; 45 46 PetscFunctionBegin; 47 PetscValidPointer(sf,2); 48 ierr = PetscSFInitializePackage();CHKERRQ(ierr); 49 50 ierr = PetscHeaderCreate(b,PETSCSF_CLASSID,"PetscSF","Star Forest","PetscSF",comm,PetscSFDestroy,PetscSFView);CHKERRQ(ierr); 51 52 b->nroots = -1; 53 b->nleaves = -1; 54 b->minleaf = PETSC_MAX_INT; 55 b->maxleaf = PETSC_MIN_INT; 56 b->nranks = -1; 57 b->rankorder = PETSC_TRUE; 58 b->ingroup = MPI_GROUP_NULL; 59 b->outgroup = MPI_GROUP_NULL; 60 b->graphset = PETSC_FALSE; 61 62 *sf = b; 63 PetscFunctionReturn(0); 64 } 65 66 /*@ 67 PetscSFReset - Reset a star forest so that different sizes or neighbors can be used 68 69 Collective 70 71 Input Arguments: 72 . sf - star forest 73 74 Level: advanced 75 76 .seealso: PetscSFCreate(), PetscSFSetGraph(), PetscSFDestroy() 77 @*/ 78 PetscErrorCode PetscSFReset(PetscSF sf) 79 { 80 PetscErrorCode ierr; 81 82 PetscFunctionBegin; 83 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 84 if (sf->ops->Reset) {ierr = (*sf->ops->Reset)(sf);CHKERRQ(ierr);} 85 sf->nroots = -1; 86 sf->nleaves = -1; 87 sf->minleaf = PETSC_MAX_INT; 88 sf->maxleaf = PETSC_MIN_INT; 89 sf->mine = NULL; 90 sf->remote = NULL; 91 sf->graphset = PETSC_FALSE; 92 ierr = PetscFree(sf->mine_alloc);CHKERRQ(ierr); 93 ierr = PetscFree(sf->remote_alloc);CHKERRQ(ierr); 94 sf->nranks = -1; 95 ierr = PetscFree4(sf->ranks,sf->roffset,sf->rmine,sf->rremote);CHKERRQ(ierr); 96 #if defined(PETSC_HAVE_CUDA) 97 if (sf->rmine_d) {cudaError_t err = cudaFree(sf->rmine_d);CHKERRCUDA(err);sf->rmine_d=NULL;} 98 #endif 99 sf->degreeknown = PETSC_FALSE; 100 ierr = PetscFree(sf->degree);CHKERRQ(ierr); 101 if (sf->ingroup != MPI_GROUP_NULL) {ierr = MPI_Group_free(&sf->ingroup);CHKERRQ(ierr);} 102 if (sf->outgroup != MPI_GROUP_NULL) {ierr = MPI_Group_free(&sf->outgroup);CHKERRQ(ierr);} 103 ierr = PetscSFDestroy(&sf->multi);CHKERRQ(ierr); 104 ierr = PetscLayoutDestroy(&sf->map);CHKERRQ(ierr); 105 sf->setupcalled = PETSC_FALSE; 106 PetscFunctionReturn(0); 107 } 108 109 /*@C 110 PetscSFSetType - Set the PetscSF communication implementation 111 112 Collective on PetscSF 113 114 Input Parameters: 115 + sf - the PetscSF context 116 - type - a known method 117 118 Options Database Key: 119 . -sf_type <type> - Sets the method; use -help for a list 120 of available methods (for instance, window, pt2pt, neighbor) 121 122 Notes: 123 See "include/petscsf.h" for available methods (for instance) 124 + PETSCSFWINDOW - MPI-2/3 one-sided 125 - PETSCSFBASIC - basic implementation using MPI-1 two-sided 126 127 Level: intermediate 128 129 .seealso: PetscSFType, PetscSFCreate() 130 @*/ 131 PetscErrorCode PetscSFSetType(PetscSF sf,PetscSFType type) 132 { 133 PetscErrorCode ierr,(*r)(PetscSF); 134 PetscBool match; 135 136 PetscFunctionBegin; 137 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 138 PetscValidCharPointer(type,2); 139 140 ierr = PetscObjectTypeCompare((PetscObject)sf,type,&match);CHKERRQ(ierr); 141 if (match) PetscFunctionReturn(0); 142 143 ierr = PetscFunctionListFind(PetscSFList,type,&r);CHKERRQ(ierr); 144 if (!r) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_UNKNOWN_TYPE,"Unable to find requested PetscSF type %s",type); 145 /* Destroy the previous PetscSF implementation context */ 146 if (sf->ops->Destroy) {ierr = (*(sf)->ops->Destroy)(sf);CHKERRQ(ierr);} 147 ierr = PetscMemzero(sf->ops,sizeof(*sf->ops));CHKERRQ(ierr); 148 ierr = PetscObjectChangeTypeName((PetscObject)sf,type);CHKERRQ(ierr); 149 ierr = (*r)(sf);CHKERRQ(ierr); 150 PetscFunctionReturn(0); 151 } 152 153 /*@C 154 PetscSFGetType - Get the PetscSF communication implementation 155 156 Not Collective 157 158 Input Parameter: 159 . sf - the PetscSF context 160 161 Output Parameter: 162 . type - the PetscSF type name 163 164 Level: intermediate 165 166 .seealso: PetscSFSetType(), PetscSFCreate() 167 @*/ 168 PetscErrorCode PetscSFGetType(PetscSF sf, PetscSFType *type) 169 { 170 PetscFunctionBegin; 171 PetscValidHeaderSpecific(sf, PETSCSF_CLASSID,1); 172 PetscValidPointer(type,2); 173 *type = ((PetscObject)sf)->type_name; 174 PetscFunctionReturn(0); 175 } 176 177 /*@ 178 PetscSFDestroy - destroy star forest 179 180 Collective 181 182 Input Arguments: 183 . sf - address of star forest 184 185 Level: intermediate 186 187 .seealso: PetscSFCreate(), PetscSFReset() 188 @*/ 189 PetscErrorCode PetscSFDestroy(PetscSF *sf) 190 { 191 PetscErrorCode ierr; 192 193 PetscFunctionBegin; 194 if (!*sf) PetscFunctionReturn(0); 195 PetscValidHeaderSpecific((*sf),PETSCSF_CLASSID,1); 196 if (--((PetscObject)(*sf))->refct > 0) {*sf = NULL; PetscFunctionReturn(0);} 197 ierr = PetscSFReset(*sf);CHKERRQ(ierr); 198 if ((*sf)->ops->Destroy) {ierr = (*(*sf)->ops->Destroy)(*sf);CHKERRQ(ierr);} 199 ierr = PetscHeaderDestroy(sf);CHKERRQ(ierr); 200 PetscFunctionReturn(0); 201 } 202 203 static PetscErrorCode PetscSFCheckGraphValid_Private(PetscSF sf) 204 { 205 #if defined(PETSC_USE_DEBUG) 206 PetscInt i, nleaves; 207 PetscMPIInt size; 208 const PetscInt *ilocal; 209 const PetscSFNode *iremote; 210 PetscErrorCode ierr; 211 212 PetscFunctionBegin; 213 if (!sf->graphset) PetscFunctionReturn(0); 214 ierr = PetscSFGetGraph(sf,NULL,&nleaves,&ilocal,&iremote);CHKERRQ(ierr); 215 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)sf),&size);CHKERRQ(ierr); 216 for (i = 0; i < nleaves; i++) { 217 const PetscInt rank = iremote[i].rank; 218 const PetscInt remote = iremote[i].index; 219 const PetscInt leaf = ilocal ? ilocal[i] : i; 220 if (rank < 0 || rank >= size) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Provided rank (%D) for remote %D is invalid, should be in [0, %d)",rank,i,size); 221 if (remote < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Provided index (%D) for remote %D is invalid, should be >= 0",remote,i); 222 if (leaf < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Provided location (%D) for leaf %D is invalid, should be >= 0",leaf,i); 223 } 224 PetscFunctionReturn(0); 225 #else 226 PetscFunctionBegin; 227 PetscFunctionReturn(0); 228 #endif 229 } 230 231 /*@ 232 PetscSFSetUp - set up communication structures 233 234 Collective 235 236 Input Arguments: 237 . sf - star forest communication object 238 239 Level: beginner 240 241 .seealso: PetscSFSetFromOptions(), PetscSFSetType() 242 @*/ 243 PetscErrorCode PetscSFSetUp(PetscSF sf) 244 { 245 PetscErrorCode ierr; 246 247 PetscFunctionBegin; 248 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 249 PetscSFCheckGraphSet(sf,1); 250 if (sf->setupcalled) PetscFunctionReturn(0); 251 ierr = PetscSFCheckGraphValid_Private(sf);CHKERRQ(ierr); 252 if (!((PetscObject)sf)->type_name) {ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr);} 253 ierr = PetscLogEventBegin(PETSCSF_SetUp,sf,0,0,0);CHKERRQ(ierr); 254 if (sf->ops->SetUp) {ierr = (*sf->ops->SetUp)(sf);CHKERRQ(ierr);} 255 ierr = PetscLogEventEnd(PETSCSF_SetUp,sf,0,0,0);CHKERRQ(ierr); 256 sf->setupcalled = PETSC_TRUE; 257 PetscFunctionReturn(0); 258 } 259 260 /*@ 261 PetscSFSetFromOptions - set PetscSF options using the options database 262 263 Logically Collective 264 265 Input Arguments: 266 . sf - star forest 267 268 Options Database Keys: 269 + -sf_type - implementation type, see PetscSFSetType() 270 . -sf_rank_order - sort composite points for gathers and scatters in rank order, gathers are non-deterministic otherwise 271 - -sf_use_pinned_buffer - use pinned (nonpagable) memory for send/recv buffers on host when communicating GPU data but GPU-aware MPI is not used. 272 Only available for SF types of basic and neighbor. 273 274 Level: intermediate 275 276 .seealso: PetscSFWindowSetSyncType() 277 @*/ 278 PetscErrorCode PetscSFSetFromOptions(PetscSF sf) 279 { 280 PetscSFType deft; 281 char type[256]; 282 PetscErrorCode ierr; 283 PetscBool flg; 284 285 PetscFunctionBegin; 286 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 287 ierr = PetscObjectOptionsBegin((PetscObject)sf);CHKERRQ(ierr); 288 deft = ((PetscObject)sf)->type_name ? ((PetscObject)sf)->type_name : PETSCSFBASIC; 289 ierr = PetscOptionsFList("-sf_type","PetscSF implementation type","PetscSFSetType",PetscSFList,deft,type,sizeof(type),&flg);CHKERRQ(ierr); 290 ierr = PetscSFSetType(sf,flg ? type : deft);CHKERRQ(ierr); 291 ierr = PetscOptionsBool("-sf_rank_order","sort composite points for gathers and scatters in rank order, gathers are non-deterministic otherwise","PetscSFSetRankOrder",sf->rankorder,&sf->rankorder,NULL);CHKERRQ(ierr); 292 if (sf->ops->SetFromOptions) {ierr = (*sf->ops->SetFromOptions)(PetscOptionsObject,sf);CHKERRQ(ierr);} 293 ierr = PetscOptionsEnd();CHKERRQ(ierr); 294 PetscFunctionReturn(0); 295 } 296 297 /*@ 298 PetscSFSetRankOrder - sort multi-points for gathers and scatters by rank order 299 300 Logically Collective 301 302 Input Arguments: 303 + sf - star forest 304 - flg - PETSC_TRUE to sort, PETSC_FALSE to skip sorting (lower setup cost, but non-deterministic) 305 306 Level: advanced 307 308 .seealso: PetscSFGatherBegin(), PetscSFScatterBegin() 309 @*/ 310 PetscErrorCode PetscSFSetRankOrder(PetscSF sf,PetscBool flg) 311 { 312 313 PetscFunctionBegin; 314 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 315 PetscValidLogicalCollectiveBool(sf,flg,2); 316 if (sf->multi) SETERRQ(PetscObjectComm((PetscObject)sf),PETSC_ERR_ARG_WRONGSTATE,"Rank ordering must be set before first call to PetscSFGatherBegin() or PetscSFScatterBegin()"); 317 sf->rankorder = flg; 318 PetscFunctionReturn(0); 319 } 320 321 /*@ 322 PetscSFSetGraph - Set a parallel star forest 323 324 Collective 325 326 Input Arguments: 327 + sf - star forest 328 . nroots - number of root vertices on the current process (these are possible targets for other process to attach leaves) 329 . nleaves - number of leaf vertices on the current process, each of these references a root on any process 330 . ilocal - locations of leaves in leafdata buffers, pass NULL for contiguous storage (locations must be >= 0, enforced 331 during setup in debug mode) 332 . localmode - copy mode for ilocal 333 . iremote - remote locations of root vertices for each leaf on the current process (locations must be >= 0, enforced 334 during setup in debug mode) 335 - remotemode - copy mode for iremote 336 337 Level: intermediate 338 339 Notes: 340 In Fortran you must use PETSC_COPY_VALUES for localmode and remotemode 341 342 Developers Note: Local indices which are the identity permutation in the range [0,nleaves) are discarded as they 343 encode contiguous storage. In such case, if localmode is PETSC_OWN_POINTER, the memory is deallocated as it is not 344 needed 345 346 Developers Note: This object does not necessarily encode a true star forest in the graph theoretic sense, since leaf 347 indices are not required to be unique. Some functions, however, rely on unique leaf indices (checked in debug mode). 348 349 .seealso: PetscSFCreate(), PetscSFView(), PetscSFGetGraph() 350 @*/ 351 PetscErrorCode PetscSFSetGraph(PetscSF sf,PetscInt nroots,PetscInt nleaves,const PetscInt *ilocal,PetscCopyMode localmode,const PetscSFNode *iremote,PetscCopyMode remotemode) 352 { 353 PetscErrorCode ierr; 354 355 PetscFunctionBegin; 356 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 357 if (nleaves > 0 && ilocal) PetscValidIntPointer(ilocal,4); 358 if (nleaves > 0) PetscValidPointer(iremote,6); 359 if (nroots < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nroots %D, cannot be negative",nroots); 360 if (nleaves < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nleaves %D, cannot be negative",nleaves); 361 362 ierr = PetscSFReset(sf);CHKERRQ(ierr); 363 ierr = PetscLogEventBegin(PETSCSF_SetGraph,sf,0,0,0);CHKERRQ(ierr); 364 365 sf->nroots = nroots; 366 sf->nleaves = nleaves; 367 368 if (nleaves && ilocal) { 369 PetscInt i; 370 PetscInt minleaf = PETSC_MAX_INT; 371 PetscInt maxleaf = PETSC_MIN_INT; 372 int contiguous = 1; 373 for (i=0; i<nleaves; i++) { 374 minleaf = PetscMin(minleaf,ilocal[i]); 375 maxleaf = PetscMax(maxleaf,ilocal[i]); 376 contiguous &= (ilocal[i] == i); 377 } 378 sf->minleaf = minleaf; 379 sf->maxleaf = maxleaf; 380 if (contiguous) { 381 if (localmode == PETSC_OWN_POINTER) { 382 ierr = PetscFree(ilocal);CHKERRQ(ierr); 383 } 384 ilocal = NULL; 385 } 386 } else { 387 sf->minleaf = 0; 388 sf->maxleaf = nleaves - 1; 389 } 390 391 if (ilocal) { 392 switch (localmode) { 393 case PETSC_COPY_VALUES: 394 ierr = PetscMalloc1(nleaves,&sf->mine_alloc);CHKERRQ(ierr); 395 ierr = PetscArraycpy(sf->mine_alloc,ilocal,nleaves);CHKERRQ(ierr); 396 sf->mine = sf->mine_alloc; 397 break; 398 case PETSC_OWN_POINTER: 399 sf->mine_alloc = (PetscInt*)ilocal; 400 sf->mine = sf->mine_alloc; 401 break; 402 case PETSC_USE_POINTER: 403 sf->mine_alloc = NULL; 404 sf->mine = (PetscInt*)ilocal; 405 break; 406 default: SETERRQ(PetscObjectComm((PetscObject)sf),PETSC_ERR_ARG_OUTOFRANGE,"Unknown localmode"); 407 } 408 } 409 410 switch (remotemode) { 411 case PETSC_COPY_VALUES: 412 ierr = PetscMalloc1(nleaves,&sf->remote_alloc);CHKERRQ(ierr); 413 ierr = PetscArraycpy(sf->remote_alloc,iremote,nleaves);CHKERRQ(ierr); 414 sf->remote = sf->remote_alloc; 415 break; 416 case PETSC_OWN_POINTER: 417 sf->remote_alloc = (PetscSFNode*)iremote; 418 sf->remote = sf->remote_alloc; 419 break; 420 case PETSC_USE_POINTER: 421 sf->remote_alloc = NULL; 422 sf->remote = (PetscSFNode*)iremote; 423 break; 424 default: SETERRQ(PetscObjectComm((PetscObject)sf),PETSC_ERR_ARG_OUTOFRANGE,"Unknown remotemode"); 425 } 426 427 ierr = PetscLogEventEnd(PETSCSF_SetGraph,sf,0,0,0);CHKERRQ(ierr); 428 sf->graphset = PETSC_TRUE; 429 PetscFunctionReturn(0); 430 } 431 432 /*@ 433 PetscSFSetGraphWithPattern - Sets the graph of an SF with a specific pattern 434 435 Collective 436 437 Input Parameters: 438 + sf - The PetscSF 439 . map - Layout of roots over all processes (insignificant when pattern is PETSCSF_PATTERN_ALLTOALL) 440 - pattern - One of PETSCSF_PATTERN_ALLGATHER, PETSCSF_PATTERN_GATHER, PETSCSF_PATTERN_ALLTOALL 441 442 Notes: 443 It is easier to explain PetscSFPattern using vectors. Suppose we have an MPI vector x and its layout is map. 444 n and N are local and global sizes of x respectively. 445 446 With PETSCSF_PATTERN_ALLGATHER, the routine creates a graph that if one does Bcast on it, it will copy x to 447 sequential vectors y on all ranks. 448 449 With PETSCSF_PATTERN_GATHER, the routine creates a graph that if one does Bcast on it, it will copy x to a 450 sequential vector y on rank 0. 451 452 In above cases, entries of x are roots and entries of y are leaves. 453 454 With PETSCSF_PATTERN_ALLTOALL, map is insignificant. Suppose NP is size of sf's communicator. The routine 455 creates a graph that every rank has NP leaves and NP roots. On rank i, its leaf j is connected to root i 456 of rank j. Here 0 <=i,j<NP. It is a kind of MPI_Alltoall with sendcount/recvcount being 1. Note that it does 457 not mean one can not send multiple items. One just needs to create a new MPI datatype for the mulptiple data 458 items with MPI_Type_contiguous() and use that as the <unit> argument in SF routines. 459 460 In this case, roots and leaves are symmetric. 461 462 Level: intermediate 463 @*/ 464 PetscErrorCode PetscSFSetGraphWithPattern(PetscSF sf,PetscLayout map,PetscSFPattern pattern) 465 { 466 MPI_Comm comm; 467 PetscInt n,N,res[2]; 468 PetscMPIInt rank,size; 469 PetscSFType type; 470 PetscErrorCode ierr; 471 472 PetscFunctionBegin; 473 ierr = PetscObjectGetComm((PetscObject)sf, &comm);CHKERRQ(ierr); 474 if (pattern < PETSCSF_PATTERN_ALLGATHER || pattern > PETSCSF_PATTERN_ALLTOALL) SETERRQ1(comm,PETSC_ERR_ARG_OUTOFRANGE,"Unsupported PetscSFPattern %D\n",pattern); 475 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 476 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 477 478 if (pattern == PETSCSF_PATTERN_ALLTOALL) { 479 type = PETSCSFALLTOALL; 480 ierr = PetscLayoutCreate(comm,&sf->map);CHKERRQ(ierr); 481 ierr = PetscLayoutSetLocalSize(sf->map,size);CHKERRQ(ierr); 482 ierr = PetscLayoutSetSize(sf->map,((PetscInt)size)*size);CHKERRQ(ierr); 483 ierr = PetscLayoutSetUp(sf->map);CHKERRQ(ierr); 484 } else { 485 ierr = PetscLayoutGetLocalSize(map,&n);CHKERRQ(ierr); 486 ierr = PetscLayoutGetSize(map,&N);CHKERRQ(ierr); 487 res[0] = n; 488 res[1] = -n; 489 /* Check if n are same over all ranks so that we can optimize it */ 490 ierr = MPIU_Allreduce(MPI_IN_PLACE,res,2,MPIU_INT,MPI_MAX,comm);CHKERRQ(ierr); 491 if (res[0] == -res[1]) { /* same n */ 492 type = (pattern == PETSCSF_PATTERN_ALLGATHER) ? PETSCSFALLGATHER : PETSCSFGATHER; 493 } else { 494 type = (pattern == PETSCSF_PATTERN_ALLGATHER) ? PETSCSFALLGATHERV : PETSCSFGATHERV; 495 } 496 ierr = PetscLayoutReference(map,&sf->map);CHKERRQ(ierr); 497 } 498 ierr = PetscSFSetType(sf,type);CHKERRQ(ierr); 499 500 sf->pattern = pattern; 501 sf->mine = NULL; /* Contiguous */ 502 503 /* Set nleaves, nroots here in case user calls PetscSFGetGraph, which is legal to call even before PetscSFSetUp is called. 504 Also set other easy stuff. 505 */ 506 if (pattern == PETSCSF_PATTERN_ALLGATHER) { 507 sf->nleaves = N; 508 sf->nroots = n; 509 sf->nranks = size; 510 sf->minleaf = 0; 511 sf->maxleaf = N - 1; 512 } else if (pattern == PETSCSF_PATTERN_GATHER) { 513 sf->nleaves = rank ? 0 : N; 514 sf->nroots = n; 515 sf->nranks = rank ? 0 : size; 516 sf->minleaf = 0; 517 sf->maxleaf = rank ? -1 : N - 1; 518 } else if (pattern == PETSCSF_PATTERN_ALLTOALL) { 519 sf->nleaves = size; 520 sf->nroots = size; 521 sf->nranks = size; 522 sf->minleaf = 0; 523 sf->maxleaf = size - 1; 524 } 525 sf->ndranks = 0; /* We do not need to separate out distinguished ranks for patterned graphs to improve communication performance */ 526 sf->graphset = PETSC_TRUE; 527 PetscFunctionReturn(0); 528 } 529 530 /*@ 531 PetscSFCreateInverseSF - given a PetscSF in which all vertices have degree 1, creates the inverse map 532 533 Collective 534 535 Input Arguments: 536 537 . sf - star forest to invert 538 539 Output Arguments: 540 . isf - inverse of sf 541 Level: advanced 542 543 Notes: 544 All roots must have degree 1. 545 546 The local space may be a permutation, but cannot be sparse. 547 548 .seealso: PetscSFSetGraph() 549 @*/ 550 PetscErrorCode PetscSFCreateInverseSF(PetscSF sf,PetscSF *isf) 551 { 552 PetscErrorCode ierr; 553 PetscMPIInt rank; 554 PetscInt i,nroots,nleaves,maxlocal,count,*newilocal; 555 const PetscInt *ilocal; 556 PetscSFNode *roots,*leaves; 557 558 PetscFunctionBegin; 559 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 560 PetscSFCheckGraphSet(sf,1); 561 PetscValidPointer(isf,2); 562 563 ierr = PetscSFGetGraph(sf,&nroots,&nleaves,&ilocal,NULL);CHKERRQ(ierr); 564 maxlocal = sf->maxleaf+1; /* TODO: We should use PetscSFGetLeafRange() */ 565 566 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)sf),&rank);CHKERRQ(ierr); 567 ierr = PetscMalloc2(nroots,&roots,maxlocal,&leaves);CHKERRQ(ierr); 568 for (i=0; i<maxlocal; i++) { 569 leaves[i].rank = rank; 570 leaves[i].index = i; 571 } 572 for (i=0; i <nroots; i++) { 573 roots[i].rank = -1; 574 roots[i].index = -1; 575 } 576 ierr = PetscSFReduceBegin(sf,MPIU_2INT,leaves,roots,MPIU_REPLACE);CHKERRQ(ierr); 577 ierr = PetscSFReduceEnd(sf,MPIU_2INT,leaves,roots,MPIU_REPLACE);CHKERRQ(ierr); 578 579 /* Check whether our leaves are sparse */ 580 for (i=0,count=0; i<nroots; i++) if (roots[i].rank >= 0) count++; 581 if (count == nroots) newilocal = NULL; 582 else { /* Index for sparse leaves and compact "roots" array (which is to become our leaves). */ 583 ierr = PetscMalloc1(count,&newilocal);CHKERRQ(ierr); 584 for (i=0,count=0; i<nroots; i++) { 585 if (roots[i].rank >= 0) { 586 newilocal[count] = i; 587 roots[count].rank = roots[i].rank; 588 roots[count].index = roots[i].index; 589 count++; 590 } 591 } 592 } 593 594 ierr = PetscSFDuplicate(sf,PETSCSF_DUPLICATE_CONFONLY,isf);CHKERRQ(ierr); 595 ierr = PetscSFSetGraph(*isf,maxlocal,count,newilocal,PETSC_OWN_POINTER,roots,PETSC_COPY_VALUES);CHKERRQ(ierr); 596 ierr = PetscFree2(roots,leaves);CHKERRQ(ierr); 597 PetscFunctionReturn(0); 598 } 599 600 /*@ 601 PetscSFDuplicate - duplicate a PetscSF, optionally preserving rank connectivity and graph 602 603 Collective 604 605 Input Arguments: 606 + sf - communication object to duplicate 607 - opt - PETSCSF_DUPLICATE_CONFONLY, PETSCSF_DUPLICATE_RANKS, or PETSCSF_DUPLICATE_GRAPH (see PetscSFDuplicateOption) 608 609 Output Arguments: 610 . newsf - new communication object 611 612 Level: beginner 613 614 .seealso: PetscSFCreate(), PetscSFSetType(), PetscSFSetGraph() 615 @*/ 616 PetscErrorCode PetscSFDuplicate(PetscSF sf,PetscSFDuplicateOption opt,PetscSF *newsf) 617 { 618 PetscSFType type; 619 PetscErrorCode ierr; 620 621 PetscFunctionBegin; 622 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 623 PetscValidLogicalCollectiveEnum(sf,opt,2); 624 PetscValidPointer(newsf,3); 625 ierr = PetscSFCreate(PetscObjectComm((PetscObject)sf),newsf);CHKERRQ(ierr); 626 ierr = PetscSFGetType(sf,&type);CHKERRQ(ierr); 627 if (type) {ierr = PetscSFSetType(*newsf,type);CHKERRQ(ierr);} 628 if (opt == PETSCSF_DUPLICATE_GRAPH) { 629 PetscSFCheckGraphSet(sf,1); 630 if (sf->pattern == PETSCSF_PATTERN_GENERAL) { 631 PetscInt nroots,nleaves; 632 const PetscInt *ilocal; 633 const PetscSFNode *iremote; 634 ierr = PetscSFGetGraph(sf,&nroots,&nleaves,&ilocal,&iremote);CHKERRQ(ierr); 635 ierr = PetscSFSetGraph(*newsf,nroots,nleaves,ilocal,PETSC_COPY_VALUES,iremote,PETSC_COPY_VALUES);CHKERRQ(ierr); 636 } else { 637 ierr = PetscSFSetGraphWithPattern(*newsf,sf->map,sf->pattern);CHKERRQ(ierr); 638 } 639 } 640 if (sf->ops->Duplicate) {ierr = (*sf->ops->Duplicate)(sf,opt,*newsf);CHKERRQ(ierr);} 641 PetscFunctionReturn(0); 642 } 643 644 /*@C 645 PetscSFGetGraph - Get the graph specifying a parallel star forest 646 647 Not Collective 648 649 Input Arguments: 650 . sf - star forest 651 652 Output Arguments: 653 + nroots - number of root vertices on the current process (these are possible targets for other process to attach leaves) 654 . nleaves - number of leaf vertices on the current process, each of these references a root on any process 655 . ilocal - locations of leaves in leafdata buffers 656 - iremote - remote locations of root vertices for each leaf on the current process 657 658 Notes: 659 We are not currently requiring that the graph is set, thus returning nroots=-1 if it has not been set yet 660 661 When called from Fortran, the returned iremote array is a copy and must deallocated after use. Consequently, if you 662 want to update the graph, you must call PetscSFSetGraph after modifying the iremote array. 663 664 Level: intermediate 665 666 .seealso: PetscSFCreate(), PetscSFView(), PetscSFSetGraph() 667 @*/ 668 PetscErrorCode PetscSFGetGraph(PetscSF sf,PetscInt *nroots,PetscInt *nleaves,const PetscInt **ilocal,const PetscSFNode **iremote) 669 { 670 PetscErrorCode ierr; 671 672 PetscFunctionBegin; 673 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 674 if (sf->ops->GetGraph) { 675 ierr = (sf->ops->GetGraph)(sf,nroots,nleaves,ilocal,iremote);CHKERRQ(ierr); 676 } else { 677 if (nroots) *nroots = sf->nroots; 678 if (nleaves) *nleaves = sf->nleaves; 679 if (ilocal) *ilocal = sf->mine; 680 if (iremote) *iremote = sf->remote; 681 } 682 PetscFunctionReturn(0); 683 } 684 685 /*@ 686 PetscSFGetLeafRange - Get the active leaf ranges 687 688 Not Collective 689 690 Input Arguments: 691 . sf - star forest 692 693 Output Arguments: 694 + minleaf - minimum active leaf on this process. Return 0 if there are no leaves. 695 - maxleaf - maximum active leaf on this process. Return -1 if there are no leaves. 696 697 Level: developer 698 699 .seealso: PetscSFCreate(), PetscSFView(), PetscSFSetGraph(), PetscSFGetGraph() 700 @*/ 701 PetscErrorCode PetscSFGetLeafRange(PetscSF sf,PetscInt *minleaf,PetscInt *maxleaf) 702 { 703 704 PetscFunctionBegin; 705 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 706 PetscSFCheckGraphSet(sf,1); 707 if (minleaf) *minleaf = sf->minleaf; 708 if (maxleaf) *maxleaf = sf->maxleaf; 709 PetscFunctionReturn(0); 710 } 711 712 /*@C 713 PetscSFViewFromOptions - View from Options 714 715 Collective on PetscSF 716 717 Input Parameters: 718 + A - the star forest 719 . obj - Optional object 720 - name - command line option 721 722 Level: intermediate 723 .seealso: PetscSF, PetscSFView, PetscObjectViewFromOptions(), PetscSFCreate() 724 @*/ 725 PetscErrorCode PetscSFViewFromOptions(PetscSF A,PetscObject obj,const char name[]) 726 { 727 PetscErrorCode ierr; 728 729 PetscFunctionBegin; 730 PetscValidHeaderSpecific(A,PETSCSF_CLASSID,1); 731 ierr = PetscObjectViewFromOptions((PetscObject)A,obj,name);CHKERRQ(ierr); 732 PetscFunctionReturn(0); 733 } 734 735 /*@C 736 PetscSFView - view a star forest 737 738 Collective 739 740 Input Arguments: 741 + sf - star forest 742 - viewer - viewer to display graph, for example PETSC_VIEWER_STDOUT_WORLD 743 744 Level: beginner 745 746 .seealso: PetscSFCreate(), PetscSFSetGraph() 747 @*/ 748 PetscErrorCode PetscSFView(PetscSF sf,PetscViewer viewer) 749 { 750 PetscErrorCode ierr; 751 PetscBool iascii; 752 PetscViewerFormat format; 753 754 PetscFunctionBegin; 755 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 756 if (!viewer) {ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)sf),&viewer);CHKERRQ(ierr);} 757 PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,2); 758 PetscCheckSameComm(sf,1,viewer,2); 759 if (sf->graphset) {ierr = PetscSFSetUp(sf);CHKERRQ(ierr);} 760 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 761 if (iascii) { 762 PetscMPIInt rank; 763 PetscInt ii,i,j; 764 765 ierr = PetscObjectPrintClassNamePrefixType((PetscObject)sf,viewer);CHKERRQ(ierr); 766 ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); 767 if (sf->ops->View) {ierr = (*sf->ops->View)(sf,viewer);CHKERRQ(ierr);} 768 if (sf->pattern == PETSCSF_PATTERN_GENERAL) { 769 if (!sf->graphset) { 770 ierr = PetscViewerASCIIPrintf(viewer,"PetscSFSetGraph() has not been called yet\n");CHKERRQ(ierr); 771 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 772 PetscFunctionReturn(0); 773 } 774 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)sf),&rank);CHKERRQ(ierr); 775 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 776 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Number of roots=%D, leaves=%D, remote ranks=%D\n",rank,sf->nroots,sf->nleaves,sf->nranks);CHKERRQ(ierr); 777 for (i=0; i<sf->nleaves; i++) { 778 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] %D <- (%D,%D)\n",rank,sf->mine ? sf->mine[i] : i,sf->remote[i].rank,sf->remote[i].index);CHKERRQ(ierr); 779 } 780 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 781 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 782 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 783 PetscMPIInt *tmpranks,*perm; 784 ierr = PetscMalloc2(sf->nranks,&tmpranks,sf->nranks,&perm);CHKERRQ(ierr); 785 ierr = PetscArraycpy(tmpranks,sf->ranks,sf->nranks);CHKERRQ(ierr); 786 for (i=0; i<sf->nranks; i++) perm[i] = i; 787 ierr = PetscSortMPIIntWithArray(sf->nranks,tmpranks,perm);CHKERRQ(ierr); 788 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Roots referenced by my leaves, by rank\n",rank);CHKERRQ(ierr); 789 for (ii=0; ii<sf->nranks; ii++) { 790 i = perm[ii]; 791 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] %d: %D edges\n",rank,sf->ranks[i],sf->roffset[i+1]-sf->roffset[i]);CHKERRQ(ierr); 792 for (j=sf->roffset[i]; j<sf->roffset[i+1]; j++) { 793 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] %D <- %D\n",rank,sf->rmine[j],sf->rremote[j]);CHKERRQ(ierr); 794 } 795 } 796 ierr = PetscFree2(tmpranks,perm);CHKERRQ(ierr); 797 } 798 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 799 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 800 } 801 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 802 } 803 PetscFunctionReturn(0); 804 } 805 806 /*@C 807 PetscSFGetRootRanks - Get root ranks and number of vertices referenced by leaves on this process 808 809 Not Collective 810 811 Input Arguments: 812 . sf - star forest 813 814 Output Arguments: 815 + nranks - number of ranks referenced by local part 816 . ranks - array of ranks 817 . roffset - offset in rmine/rremote for each rank (length nranks+1) 818 . rmine - concatenated array holding local indices referencing each remote rank 819 - rremote - concatenated array holding remote indices referenced for each remote rank 820 821 Level: developer 822 823 .seealso: PetscSFGetLeafRanks() 824 @*/ 825 PetscErrorCode PetscSFGetRootRanks(PetscSF sf,PetscInt *nranks,const PetscMPIInt **ranks,const PetscInt **roffset,const PetscInt **rmine,const PetscInt **rremote) 826 { 827 PetscErrorCode ierr; 828 829 PetscFunctionBegin; 830 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 831 if (!sf->setupcalled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call PetscSFSetUp() before obtaining ranks"); 832 if (sf->ops->GetRootRanks) { 833 ierr = (sf->ops->GetRootRanks)(sf,nranks,ranks,roffset,rmine,rremote);CHKERRQ(ierr); 834 } else { 835 /* The generic implementation */ 836 if (nranks) *nranks = sf->nranks; 837 if (ranks) *ranks = sf->ranks; 838 if (roffset) *roffset = sf->roffset; 839 if (rmine) *rmine = sf->rmine; 840 if (rremote) *rremote = sf->rremote; 841 } 842 PetscFunctionReturn(0); 843 } 844 845 /*@C 846 PetscSFGetLeafRanks - Get leaf ranks referencing roots on this process 847 848 Not Collective 849 850 Input Arguments: 851 . sf - star forest 852 853 Output Arguments: 854 + niranks - number of leaf ranks referencing roots on this process 855 . iranks - array of ranks 856 . ioffset - offset in irootloc for each rank (length niranks+1) 857 - irootloc - concatenated array holding local indices of roots referenced by each leaf rank 858 859 Level: developer 860 861 .seealso: PetscSFGetRootRanks() 862 @*/ 863 PetscErrorCode PetscSFGetLeafRanks(PetscSF sf,PetscInt *niranks,const PetscMPIInt **iranks,const PetscInt **ioffset,const PetscInt **irootloc) 864 { 865 PetscErrorCode ierr; 866 867 PetscFunctionBegin; 868 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 869 if (!sf->setupcalled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call PetscSFSetUp() before obtaining ranks"); 870 if (sf->ops->GetLeafRanks) { 871 ierr = (sf->ops->GetLeafRanks)(sf,niranks,iranks,ioffset,irootloc);CHKERRQ(ierr); 872 } else { 873 PetscSFType type; 874 ierr = PetscSFGetType(sf,&type);CHKERRQ(ierr); 875 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"PetscSFGetLeafRanks() is not supported on this StarForest type: %s", type); 876 } 877 PetscFunctionReturn(0); 878 } 879 880 static PetscBool InList(PetscMPIInt needle,PetscMPIInt n,const PetscMPIInt *list) { 881 PetscInt i; 882 for (i=0; i<n; i++) { 883 if (needle == list[i]) return PETSC_TRUE; 884 } 885 return PETSC_FALSE; 886 } 887 888 /*@C 889 PetscSFSetUpRanks - Set up data structures associated with ranks; this is for internal use by PetscSF implementations. 890 891 Collective 892 893 Input Arguments: 894 + sf - PetscSF to set up; PetscSFSetGraph() must have been called 895 - dgroup - MPI_Group of ranks to be distinguished (e.g., for self or shared memory exchange) 896 897 Level: developer 898 899 .seealso: PetscSFGetRootRanks() 900 @*/ 901 PetscErrorCode PetscSFSetUpRanks(PetscSF sf,MPI_Group dgroup) 902 { 903 PetscErrorCode ierr; 904 PetscTable table; 905 PetscTablePosition pos; 906 PetscMPIInt size,groupsize,*groupranks; 907 PetscInt *rcount,*ranks; 908 PetscInt i, irank = -1,orank = -1; 909 910 PetscFunctionBegin; 911 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 912 PetscSFCheckGraphSet(sf,1); 913 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)sf),&size);CHKERRQ(ierr); 914 ierr = PetscTableCreate(10,size,&table);CHKERRQ(ierr); 915 for (i=0; i<sf->nleaves; i++) { 916 /* Log 1-based rank */ 917 ierr = PetscTableAdd(table,sf->remote[i].rank+1,1,ADD_VALUES);CHKERRQ(ierr); 918 } 919 ierr = PetscTableGetCount(table,&sf->nranks);CHKERRQ(ierr); 920 ierr = PetscMalloc4(sf->nranks,&sf->ranks,sf->nranks+1,&sf->roffset,sf->nleaves,&sf->rmine,sf->nleaves,&sf->rremote);CHKERRQ(ierr); 921 ierr = PetscMalloc2(sf->nranks,&rcount,sf->nranks,&ranks);CHKERRQ(ierr); 922 ierr = PetscTableGetHeadPosition(table,&pos);CHKERRQ(ierr); 923 for (i=0; i<sf->nranks; i++) { 924 ierr = PetscTableGetNext(table,&pos,&ranks[i],&rcount[i]);CHKERRQ(ierr); 925 ranks[i]--; /* Convert back to 0-based */ 926 } 927 ierr = PetscTableDestroy(&table);CHKERRQ(ierr); 928 929 /* We expect that dgroup is reliably "small" while nranks could be large */ 930 { 931 MPI_Group group = MPI_GROUP_NULL; 932 PetscMPIInt *dgroupranks; 933 ierr = MPI_Comm_group(PetscObjectComm((PetscObject)sf),&group);CHKERRQ(ierr); 934 ierr = MPI_Group_size(dgroup,&groupsize);CHKERRQ(ierr); 935 ierr = PetscMalloc1(groupsize,&dgroupranks);CHKERRQ(ierr); 936 ierr = PetscMalloc1(groupsize,&groupranks);CHKERRQ(ierr); 937 for (i=0; i<groupsize; i++) dgroupranks[i] = i; 938 if (groupsize) {ierr = MPI_Group_translate_ranks(dgroup,groupsize,dgroupranks,group,groupranks);CHKERRQ(ierr);} 939 ierr = MPI_Group_free(&group);CHKERRQ(ierr); 940 ierr = PetscFree(dgroupranks);CHKERRQ(ierr); 941 } 942 943 /* Partition ranks[] into distinguished (first sf->ndranks) followed by non-distinguished */ 944 for (sf->ndranks=0,i=sf->nranks; sf->ndranks<i; ) { 945 for (i--; sf->ndranks<i; i--) { /* Scan i backward looking for distinguished rank */ 946 if (InList(ranks[i],groupsize,groupranks)) break; 947 } 948 for ( ; sf->ndranks<=i; sf->ndranks++) { /* Scan sf->ndranks forward looking for non-distinguished rank */ 949 if (!InList(ranks[sf->ndranks],groupsize,groupranks)) break; 950 } 951 if (sf->ndranks < i) { /* Swap ranks[sf->ndranks] with ranks[i] */ 952 PetscInt tmprank,tmpcount; 953 954 tmprank = ranks[i]; 955 tmpcount = rcount[i]; 956 ranks[i] = ranks[sf->ndranks]; 957 rcount[i] = rcount[sf->ndranks]; 958 ranks[sf->ndranks] = tmprank; 959 rcount[sf->ndranks] = tmpcount; 960 sf->ndranks++; 961 } 962 } 963 ierr = PetscFree(groupranks);CHKERRQ(ierr); 964 ierr = PetscSortIntWithArray(sf->ndranks,ranks,rcount);CHKERRQ(ierr); 965 ierr = PetscSortIntWithArray(sf->nranks-sf->ndranks,ranks+sf->ndranks,rcount+sf->ndranks);CHKERRQ(ierr); 966 sf->roffset[0] = 0; 967 for (i=0; i<sf->nranks; i++) { 968 ierr = PetscMPIIntCast(ranks[i],sf->ranks+i);CHKERRQ(ierr); 969 sf->roffset[i+1] = sf->roffset[i] + rcount[i]; 970 rcount[i] = 0; 971 } 972 for (i=0, irank = -1, orank = -1; i<sf->nleaves; i++) { 973 /* short circuit */ 974 if (orank != sf->remote[i].rank) { 975 /* Search for index of iremote[i].rank in sf->ranks */ 976 ierr = PetscFindMPIInt(sf->remote[i].rank,sf->ndranks,sf->ranks,&irank);CHKERRQ(ierr); 977 if (irank < 0) { 978 ierr = PetscFindMPIInt(sf->remote[i].rank,sf->nranks-sf->ndranks,sf->ranks+sf->ndranks,&irank);CHKERRQ(ierr); 979 if (irank >= 0) irank += sf->ndranks; 980 } 981 orank = sf->remote[i].rank; 982 } 983 if (irank < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Could not find rank %D in array",sf->remote[i].rank); 984 sf->rmine[sf->roffset[irank] + rcount[irank]] = sf->mine ? sf->mine[i] : i; 985 sf->rremote[sf->roffset[irank] + rcount[irank]] = sf->remote[i].index; 986 rcount[irank]++; 987 } 988 ierr = PetscFree2(rcount,ranks);CHKERRQ(ierr); 989 PetscFunctionReturn(0); 990 } 991 992 /*@C 993 PetscSFGetGroups - gets incoming and outgoing process groups 994 995 Collective 996 997 Input Argument: 998 . sf - star forest 999 1000 Output Arguments: 1001 + incoming - group of origin processes for incoming edges (leaves that reference my roots) 1002 - outgoing - group of destination processes for outgoing edges (roots that I reference) 1003 1004 Level: developer 1005 1006 .seealso: PetscSFGetWindow(), PetscSFRestoreWindow() 1007 @*/ 1008 PetscErrorCode PetscSFGetGroups(PetscSF sf,MPI_Group *incoming,MPI_Group *outgoing) 1009 { 1010 PetscErrorCode ierr; 1011 MPI_Group group = MPI_GROUP_NULL; 1012 1013 PetscFunctionBegin; 1014 if (!sf->setupcalled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call PetscSFSetUp() before obtaining groups"); 1015 if (sf->ingroup == MPI_GROUP_NULL) { 1016 PetscInt i; 1017 const PetscInt *indegree; 1018 PetscMPIInt rank,*outranks,*inranks; 1019 PetscSFNode *remote; 1020 PetscSF bgcount; 1021 1022 /* Compute the number of incoming ranks */ 1023 ierr = PetscMalloc1(sf->nranks,&remote);CHKERRQ(ierr); 1024 for (i=0; i<sf->nranks; i++) { 1025 remote[i].rank = sf->ranks[i]; 1026 remote[i].index = 0; 1027 } 1028 ierr = PetscSFDuplicate(sf,PETSCSF_DUPLICATE_CONFONLY,&bgcount);CHKERRQ(ierr); 1029 ierr = PetscSFSetGraph(bgcount,1,sf->nranks,NULL,PETSC_COPY_VALUES,remote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1030 ierr = PetscSFComputeDegreeBegin(bgcount,&indegree);CHKERRQ(ierr); 1031 ierr = PetscSFComputeDegreeEnd(bgcount,&indegree);CHKERRQ(ierr); 1032 1033 /* Enumerate the incoming ranks */ 1034 ierr = PetscMalloc2(indegree[0],&inranks,sf->nranks,&outranks);CHKERRQ(ierr); 1035 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)sf),&rank);CHKERRQ(ierr); 1036 for (i=0; i<sf->nranks; i++) outranks[i] = rank; 1037 ierr = PetscSFGatherBegin(bgcount,MPI_INT,outranks,inranks);CHKERRQ(ierr); 1038 ierr = PetscSFGatherEnd(bgcount,MPI_INT,outranks,inranks);CHKERRQ(ierr); 1039 ierr = MPI_Comm_group(PetscObjectComm((PetscObject)sf),&group);CHKERRQ(ierr); 1040 ierr = MPI_Group_incl(group,indegree[0],inranks,&sf->ingroup);CHKERRQ(ierr); 1041 ierr = MPI_Group_free(&group);CHKERRQ(ierr); 1042 ierr = PetscFree2(inranks,outranks);CHKERRQ(ierr); 1043 ierr = PetscSFDestroy(&bgcount);CHKERRQ(ierr); 1044 } 1045 *incoming = sf->ingroup; 1046 1047 if (sf->outgroup == MPI_GROUP_NULL) { 1048 ierr = MPI_Comm_group(PetscObjectComm((PetscObject)sf),&group);CHKERRQ(ierr); 1049 ierr = MPI_Group_incl(group,sf->nranks,sf->ranks,&sf->outgroup);CHKERRQ(ierr); 1050 ierr = MPI_Group_free(&group);CHKERRQ(ierr); 1051 } 1052 *outgoing = sf->outgroup; 1053 PetscFunctionReturn(0); 1054 } 1055 1056 /*@ 1057 PetscSFGetMultiSF - gets the inner SF implemeting gathers and scatters 1058 1059 Collective 1060 1061 Input Argument: 1062 . sf - star forest that may contain roots with 0 or with more than 1 vertex 1063 1064 Output Arguments: 1065 . multi - star forest with split roots, such that each root has degree exactly 1 1066 1067 Level: developer 1068 1069 Notes: 1070 1071 In most cases, users should use PetscSFGatherBegin() and PetscSFScatterBegin() instead of manipulating multi 1072 directly. Since multi satisfies the stronger condition that each entry in the global space has exactly one incoming 1073 edge, it is a candidate for future optimization that might involve its removal. 1074 1075 .seealso: PetscSFSetGraph(), PetscSFGatherBegin(), PetscSFScatterBegin(), PetscSFComputeMultiRootOriginalNumbering() 1076 @*/ 1077 PetscErrorCode PetscSFGetMultiSF(PetscSF sf,PetscSF *multi) 1078 { 1079 PetscErrorCode ierr; 1080 1081 PetscFunctionBegin; 1082 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1083 PetscValidPointer(multi,2); 1084 if (sf->nroots < 0) { /* Graph has not been set yet; why do we need this? */ 1085 ierr = PetscSFDuplicate(sf,PETSCSF_DUPLICATE_RANKS,&sf->multi);CHKERRQ(ierr); 1086 *multi = sf->multi; 1087 PetscFunctionReturn(0); 1088 } 1089 if (!sf->multi) { 1090 const PetscInt *indegree; 1091 PetscInt i,*inoffset,*outones,*outoffset,maxlocal; 1092 PetscSFNode *remote; 1093 maxlocal = sf->maxleaf+1; /* TODO: We should use PetscSFGetLeafRange() */ 1094 ierr = PetscSFComputeDegreeBegin(sf,&indegree);CHKERRQ(ierr); 1095 ierr = PetscSFComputeDegreeEnd(sf,&indegree);CHKERRQ(ierr); 1096 ierr = PetscMalloc3(sf->nroots+1,&inoffset,maxlocal,&outones,maxlocal,&outoffset);CHKERRQ(ierr); 1097 inoffset[0] = 0; 1098 for (i=0; i<sf->nroots; i++) inoffset[i+1] = inoffset[i] + indegree[i]; 1099 for (i=0; i<maxlocal; i++) outones[i] = 1; 1100 ierr = PetscSFFetchAndOpBegin(sf,MPIU_INT,inoffset,outones,outoffset,MPI_SUM);CHKERRQ(ierr); 1101 ierr = PetscSFFetchAndOpEnd(sf,MPIU_INT,inoffset,outones,outoffset,MPI_SUM);CHKERRQ(ierr); 1102 for (i=0; i<sf->nroots; i++) inoffset[i] -= indegree[i]; /* Undo the increment */ 1103 #if 0 1104 #if defined(PETSC_USE_DEBUG) /* Check that the expected number of increments occurred */ 1105 for (i=0; i<sf->nroots; i++) { 1106 if (inoffset[i] + indegree[i] != inoffset[i+1]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect result after PetscSFFetchAndOp"); 1107 } 1108 #endif 1109 #endif 1110 ierr = PetscMalloc1(sf->nleaves,&remote);CHKERRQ(ierr); 1111 for (i=0; i<sf->nleaves; i++) { 1112 remote[i].rank = sf->remote[i].rank; 1113 remote[i].index = outoffset[sf->mine ? sf->mine[i] : i]; 1114 } 1115 ierr = PetscSFDuplicate(sf,PETSCSF_DUPLICATE_RANKS,&sf->multi);CHKERRQ(ierr); 1116 ierr = PetscSFSetGraph(sf->multi,inoffset[sf->nroots],sf->nleaves,sf->mine,PETSC_COPY_VALUES,remote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1117 if (sf->rankorder) { /* Sort the ranks */ 1118 PetscMPIInt rank; 1119 PetscInt *inranks,*newoffset,*outranks,*newoutoffset,*tmpoffset,maxdegree; 1120 PetscSFNode *newremote; 1121 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)sf),&rank);CHKERRQ(ierr); 1122 for (i=0,maxdegree=0; i<sf->nroots; i++) maxdegree = PetscMax(maxdegree,indegree[i]); 1123 ierr = PetscMalloc5(sf->multi->nroots,&inranks,sf->multi->nroots,&newoffset,maxlocal,&outranks,maxlocal,&newoutoffset,maxdegree,&tmpoffset);CHKERRQ(ierr); 1124 for (i=0; i<maxlocal; i++) outranks[i] = rank; 1125 ierr = PetscSFReduceBegin(sf->multi,MPIU_INT,outranks,inranks,MPIU_REPLACE);CHKERRQ(ierr); 1126 ierr = PetscSFReduceEnd(sf->multi,MPIU_INT,outranks,inranks,MPIU_REPLACE);CHKERRQ(ierr); 1127 /* Sort the incoming ranks at each vertex, build the inverse map */ 1128 for (i=0; i<sf->nroots; i++) { 1129 PetscInt j; 1130 for (j=0; j<indegree[i]; j++) tmpoffset[j] = j; 1131 ierr = PetscSortIntWithArray(indegree[i],inranks+inoffset[i],tmpoffset);CHKERRQ(ierr); 1132 for (j=0; j<indegree[i]; j++) newoffset[inoffset[i] + tmpoffset[j]] = inoffset[i] + j; 1133 } 1134 ierr = PetscSFBcastBegin(sf->multi,MPIU_INT,newoffset,newoutoffset);CHKERRQ(ierr); 1135 ierr = PetscSFBcastEnd(sf->multi,MPIU_INT,newoffset,newoutoffset);CHKERRQ(ierr); 1136 ierr = PetscMalloc1(sf->nleaves,&newremote);CHKERRQ(ierr); 1137 for (i=0; i<sf->nleaves; i++) { 1138 newremote[i].rank = sf->remote[i].rank; 1139 newremote[i].index = newoutoffset[sf->mine ? sf->mine[i] : i]; 1140 } 1141 ierr = PetscSFSetGraph(sf->multi,inoffset[sf->nroots],sf->nleaves,sf->mine,PETSC_COPY_VALUES,newremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1142 ierr = PetscFree5(inranks,newoffset,outranks,newoutoffset,tmpoffset);CHKERRQ(ierr); 1143 } 1144 ierr = PetscFree3(inoffset,outones,outoffset);CHKERRQ(ierr); 1145 } 1146 *multi = sf->multi; 1147 PetscFunctionReturn(0); 1148 } 1149 1150 /*@C 1151 PetscSFCreateEmbeddedSF - removes edges from all but the selected roots, does not remap indices 1152 1153 Collective 1154 1155 Input Arguments: 1156 + sf - original star forest 1157 . nselected - number of selected roots on this process 1158 - selected - indices of the selected roots on this process 1159 1160 Output Arguments: 1161 . newsf - new star forest 1162 1163 Level: advanced 1164 1165 Note: 1166 To use the new PetscSF, it may be necessary to know the indices of the leaves that are still participating. This can 1167 be done by calling PetscSFGetGraph(). 1168 1169 .seealso: PetscSFSetGraph(), PetscSFGetGraph() 1170 @*/ 1171 PetscErrorCode PetscSFCreateEmbeddedSF(PetscSF sf,PetscInt nselected,const PetscInt *selected,PetscSF *newsf) 1172 { 1173 PetscInt i,n,*roots,*rootdata,*leafdata,nroots,nleaves,connected_leaves,*new_ilocal; 1174 const PetscSFNode *iremote; 1175 PetscSFNode *new_iremote; 1176 PetscSF tmpsf; 1177 MPI_Comm comm; 1178 PetscErrorCode ierr; 1179 1180 PetscFunctionBegin; 1181 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1182 PetscSFCheckGraphSet(sf,1); 1183 if (nselected) PetscValidPointer(selected,3); 1184 PetscValidPointer(newsf,4); 1185 1186 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1187 ierr = PetscLogEventBegin(PETSCSF_EmbedSF,sf,0,0,0);CHKERRQ(ierr); 1188 /* Uniq selected[] and put results in roots[] */ 1189 ierr = PetscObjectGetComm((PetscObject)sf,&comm);CHKERRQ(ierr); 1190 ierr = PetscMalloc1(nselected,&roots);CHKERRQ(ierr); 1191 ierr = PetscArraycpy(roots,selected,nselected);CHKERRQ(ierr); 1192 ierr = PetscSortedRemoveDupsInt(&nselected,roots);CHKERRQ(ierr); 1193 if (nselected && (roots[0] < 0 || roots[nselected-1] >= sf->nroots)) SETERRQ3(comm,PETSC_ERR_ARG_OUTOFRANGE,"Min/Max root indices %D/%D are not in [0,%D)",roots[0],roots[nselected-1],sf->nroots); 1194 1195 if (sf->ops->CreateEmbeddedSF) { 1196 ierr = (*sf->ops->CreateEmbeddedSF)(sf,nselected,roots,newsf);CHKERRQ(ierr); 1197 } else { 1198 /* A generic version of creating embedded sf. Note that we called PetscSFSetGraph() twice, which is certainly expensive */ 1199 /* Find out which leaves (not leaf data items) are still connected to roots in the embedded sf */ 1200 ierr = PetscSFGetGraph(sf,&nroots,&nleaves,NULL,&iremote);CHKERRQ(ierr); 1201 ierr = PetscSFDuplicate(sf,PETSCSF_DUPLICATE_RANKS,&tmpsf);CHKERRQ(ierr); 1202 ierr = PetscSFSetGraph(tmpsf,nroots,nleaves,NULL/*contiguous*/,PETSC_USE_POINTER,iremote,PETSC_USE_POINTER);CHKERRQ(ierr); 1203 ierr = PetscCalloc2(nroots,&rootdata,nleaves,&leafdata);CHKERRQ(ierr); 1204 for (i=0; i<nselected; ++i) rootdata[roots[i]] = 1; 1205 ierr = PetscSFBcastBegin(tmpsf,MPIU_INT,rootdata,leafdata);CHKERRQ(ierr); 1206 ierr = PetscSFBcastEnd(tmpsf,MPIU_INT,rootdata,leafdata);CHKERRQ(ierr); 1207 ierr = PetscSFDestroy(&tmpsf);CHKERRQ(ierr); 1208 1209 /* Build newsf with leaves that are still connected */ 1210 connected_leaves = 0; 1211 for (i=0; i<nleaves; ++i) connected_leaves += leafdata[i]; 1212 ierr = PetscMalloc1(connected_leaves,&new_ilocal);CHKERRQ(ierr); 1213 ierr = PetscMalloc1(connected_leaves,&new_iremote);CHKERRQ(ierr); 1214 for (i=0, n=0; i<nleaves; ++i) { 1215 if (leafdata[i]) { 1216 new_ilocal[n] = sf->mine ? sf->mine[i] : i; 1217 new_iremote[n].rank = sf->remote[i].rank; 1218 new_iremote[n].index = sf->remote[i].index; 1219 ++n; 1220 } 1221 } 1222 1223 if (n != connected_leaves) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"There is a size mismatch in the SF embedding, %d != %d",n,connected_leaves); 1224 ierr = PetscSFCreate(comm,newsf);CHKERRQ(ierr); 1225 ierr = PetscSFSetFromOptions(*newsf);CHKERRQ(ierr); 1226 ierr = PetscSFSetGraph(*newsf,nroots,connected_leaves,new_ilocal,PETSC_OWN_POINTER,new_iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1227 ierr = PetscFree2(rootdata,leafdata);CHKERRQ(ierr); 1228 } 1229 ierr = PetscFree(roots);CHKERRQ(ierr); 1230 ierr = PetscSFSetUp(*newsf);CHKERRQ(ierr); 1231 ierr = PetscLogEventEnd(PETSCSF_EmbedSF,sf,0,0,0);CHKERRQ(ierr); 1232 PetscFunctionReturn(0); 1233 } 1234 1235 /*@C 1236 PetscSFCreateEmbeddedLeafSF - removes edges from all but the selected leaves, does not remap indices 1237 1238 Collective 1239 1240 Input Arguments: 1241 + sf - original star forest 1242 . nselected - number of selected leaves on this process 1243 - selected - indices of the selected leaves on this process 1244 1245 Output Arguments: 1246 . newsf - new star forest 1247 1248 Level: advanced 1249 1250 .seealso: PetscSFCreateEmbeddedSF(), PetscSFSetGraph(), PetscSFGetGraph() 1251 @*/ 1252 PetscErrorCode PetscSFCreateEmbeddedLeafSF(PetscSF sf,PetscInt nselected,const PetscInt *selected,PetscSF *newsf) 1253 { 1254 const PetscSFNode *iremote; 1255 PetscSFNode *new_iremote; 1256 const PetscInt *ilocal; 1257 PetscInt i,nroots,*leaves,*new_ilocal; 1258 MPI_Comm comm; 1259 PetscErrorCode ierr; 1260 1261 PetscFunctionBegin; 1262 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1263 PetscSFCheckGraphSet(sf,1); 1264 if (nselected) PetscValidPointer(selected,3); 1265 PetscValidPointer(newsf,4); 1266 1267 /* Uniq selected[] and put results in leaves[] */ 1268 ierr = PetscObjectGetComm((PetscObject)sf,&comm);CHKERRQ(ierr); 1269 ierr = PetscMalloc1(nselected,&leaves);CHKERRQ(ierr); 1270 ierr = PetscArraycpy(leaves,selected,nselected);CHKERRQ(ierr); 1271 ierr = PetscSortedRemoveDupsInt(&nselected,leaves);CHKERRQ(ierr); 1272 if (nselected && (leaves[0] < 0 || leaves[nselected-1] >= sf->nleaves)) SETERRQ3(comm,PETSC_ERR_ARG_OUTOFRANGE,"Min/Max leaf indices %D/%D are not in [0,%D)",leaves[0],leaves[nselected-1],sf->nleaves); 1273 1274 /* Optimize the routine only when sf is setup and hence we can reuse sf's communication pattern */ 1275 if (sf->setupcalled && sf->ops->CreateEmbeddedLeafSF) { 1276 ierr = (*sf->ops->CreateEmbeddedLeafSF)(sf,nselected,leaves,newsf);CHKERRQ(ierr); 1277 } else { 1278 ierr = PetscSFGetGraph(sf,&nroots,NULL,&ilocal,&iremote);CHKERRQ(ierr); 1279 ierr = PetscMalloc1(nselected,&new_ilocal);CHKERRQ(ierr); 1280 ierr = PetscMalloc1(nselected,&new_iremote);CHKERRQ(ierr); 1281 for (i=0; i<nselected; ++i) { 1282 const PetscInt l = leaves[i]; 1283 new_ilocal[i] = ilocal ? ilocal[l] : l; 1284 new_iremote[i].rank = iremote[l].rank; 1285 new_iremote[i].index = iremote[l].index; 1286 } 1287 ierr = PetscSFCreate(comm,newsf);CHKERRQ(ierr); 1288 ierr = PetscSFSetFromOptions(*newsf);CHKERRQ(ierr); 1289 ierr = PetscSFSetGraph(*newsf,nroots,nselected,new_ilocal,PETSC_OWN_POINTER,new_iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1290 } 1291 ierr = PetscFree(leaves);CHKERRQ(ierr); 1292 PetscFunctionReturn(0); 1293 } 1294 1295 /*@C 1296 PetscSFBcastAndOpBegin - begin pointwise broadcast with root value being reduced to leaf value, to be concluded with call to PetscSFBcastAndOpEnd() 1297 1298 Collective on PetscSF 1299 1300 Input Arguments: 1301 + sf - star forest on which to communicate 1302 . unit - data type associated with each node 1303 . rootdata - buffer to broadcast 1304 - op - operation to use for reduction 1305 1306 Output Arguments: 1307 . leafdata - buffer to be reduced with values from each leaf's respective root 1308 1309 Level: intermediate 1310 1311 .seealso: PetscSFBcastAndOpEnd(), PetscSFBcastBegin(), PetscSFBcastEnd() 1312 @*/ 1313 PetscErrorCode PetscSFBcastAndOpBegin(PetscSF sf,MPI_Datatype unit,const void *rootdata,void *leafdata,MPI_Op op) 1314 { 1315 PetscErrorCode ierr; 1316 PetscMemType rootmtype,leafmtype; 1317 1318 PetscFunctionBegin; 1319 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1320 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1321 ierr = PetscLogEventBegin(PETSCSF_BcastAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 1322 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1323 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1324 #if defined(PETSC_HAVE_CUDA) 1325 /* Shall we assume rootdata, leafdata are ready to use (instead of being computed by some asynchronous kernels)? 1326 To be similar to MPI, I'd like to have this assumption, since MPI does not have a concept of stream. 1327 But currently this assumption is not enforecd in Petsc. To be safe, I do synchronization here. Otherwise, if 1328 we do not sync now and call the Pack kernel directly on the default NULL stream (assume petsc objects are also 1329 computed on it), we have to sync the NULL stream before calling MPI routines. So, it looks a cudaDeviceSynchronize 1330 is inevitable. We do it now and put pack/unpack kernels to non-NULL streams. 1331 */ 1332 if (rootmtype == PETSC_MEMTYPE_DEVICE || leafmtype == PETSC_MEMTYPE_DEVICE) {cudaError_t err = cudaDeviceSynchronize();CHKERRCUDA(err);} 1333 #endif 1334 ierr = (*sf->ops->BcastAndOpBegin)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,op);CHKERRQ(ierr); 1335 ierr = PetscLogEventEnd(PETSCSF_BcastAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 1336 PetscFunctionReturn(0); 1337 } 1338 1339 /*@C 1340 PetscSFBcastAndOpEnd - end a broadcast & reduce operation started with PetscSFBcastAndOpBegin() 1341 1342 Collective 1343 1344 Input Arguments: 1345 + sf - star forest 1346 . unit - data type 1347 . rootdata - buffer to broadcast 1348 - op - operation to use for reduction 1349 1350 Output Arguments: 1351 . leafdata - buffer to be reduced with values from each leaf's respective root 1352 1353 Level: intermediate 1354 1355 .seealso: PetscSFSetGraph(), PetscSFReduceEnd() 1356 @*/ 1357 PetscErrorCode PetscSFBcastAndOpEnd(PetscSF sf,MPI_Datatype unit,const void *rootdata,void *leafdata,MPI_Op op) 1358 { 1359 PetscErrorCode ierr; 1360 PetscMemType rootmtype,leafmtype; 1361 1362 PetscFunctionBegin; 1363 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1364 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1365 ierr = PetscLogEventBegin(PETSCSF_BcastAndOpEnd,sf,0,0,0);CHKERRQ(ierr); 1366 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1367 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1368 ierr = (*sf->ops->BcastAndOpEnd)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,op);CHKERRQ(ierr); 1369 ierr = PetscLogEventEnd(PETSCSF_BcastAndOpEnd,sf,0,0,0);CHKERRQ(ierr); 1370 PetscFunctionReturn(0); 1371 } 1372 1373 /*@C 1374 PetscSFReduceBegin - begin reduction of leafdata into rootdata, to be completed with call to PetscSFReduceEnd() 1375 1376 Collective 1377 1378 Input Arguments: 1379 + sf - star forest 1380 . unit - data type 1381 . leafdata - values to reduce 1382 - op - reduction operation 1383 1384 Output Arguments: 1385 . rootdata - result of reduction of values from all leaves of each root 1386 1387 Level: intermediate 1388 1389 .seealso: PetscSFBcastBegin() 1390 @*/ 1391 PetscErrorCode PetscSFReduceBegin(PetscSF sf,MPI_Datatype unit,const void *leafdata,void *rootdata,MPI_Op op) 1392 { 1393 PetscErrorCode ierr; 1394 PetscMemType rootmtype,leafmtype; 1395 1396 PetscFunctionBegin; 1397 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1398 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1399 ierr = PetscLogEventBegin(PETSCSF_ReduceBegin,sf,0,0,0);CHKERRQ(ierr); 1400 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1401 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1402 #if defined(PETSC_HAVE_CUDA) 1403 if (rootmtype == PETSC_MEMTYPE_DEVICE || leafmtype == PETSC_MEMTYPE_DEVICE) {cudaError_t err = cudaDeviceSynchronize();CHKERRCUDA(err);} 1404 #endif 1405 ierr = (sf->ops->ReduceBegin)(sf,unit,leafmtype,leafdata,rootmtype,rootdata,op);CHKERRQ(ierr); 1406 ierr = PetscLogEventEnd(PETSCSF_ReduceBegin,sf,0,0,0);CHKERRQ(ierr); 1407 PetscFunctionReturn(0); 1408 } 1409 1410 /*@C 1411 PetscSFReduceEnd - end a reduction operation started with PetscSFReduceBegin() 1412 1413 Collective 1414 1415 Input Arguments: 1416 + sf - star forest 1417 . unit - data type 1418 . leafdata - values to reduce 1419 - op - reduction operation 1420 1421 Output Arguments: 1422 . rootdata - result of reduction of values from all leaves of each root 1423 1424 Level: intermediate 1425 1426 .seealso: PetscSFSetGraph(), PetscSFBcastEnd() 1427 @*/ 1428 PetscErrorCode PetscSFReduceEnd(PetscSF sf,MPI_Datatype unit,const void *leafdata,void *rootdata,MPI_Op op) 1429 { 1430 PetscErrorCode ierr; 1431 PetscMemType rootmtype,leafmtype; 1432 1433 PetscFunctionBegin; 1434 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1435 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1436 ierr = PetscLogEventBegin(PETSCSF_ReduceEnd,sf,0,0,0);CHKERRQ(ierr); 1437 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1438 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1439 ierr = (*sf->ops->ReduceEnd)(sf,unit,leafmtype,leafdata,rootmtype,rootdata,op);CHKERRQ(ierr); 1440 ierr = PetscLogEventEnd(PETSCSF_ReduceEnd,sf,0,0,0);CHKERRQ(ierr); 1441 PetscFunctionReturn(0); 1442 } 1443 1444 /*@C 1445 PetscSFFetchAndOpBegin - begin operation that fetches values from root and updates atomically by applying operation using my leaf value, to be completed with PetscSFFetchAndOpEnd() 1446 1447 Collective 1448 1449 Input Arguments: 1450 + sf - star forest 1451 . unit - data type 1452 . leafdata - leaf values to use in reduction 1453 - op - operation to use for reduction 1454 1455 Output Arguments: 1456 + rootdata - root values to be updated, input state is seen by first process to perform an update 1457 - leafupdate - state at each leaf's respective root immediately prior to my atomic update 1458 1459 Level: advanced 1460 1461 Note: 1462 The update is only atomic at the granularity provided by the hardware. Different roots referenced by the same process 1463 might be updated in a different order. Furthermore, if a composite type is used for the unit datatype, atomicity is 1464 not guaranteed across the whole vertex. Therefore, this function is mostly only used with primitive types such as 1465 integers. 1466 1467 .seealso: PetscSFComputeDegreeBegin(), PetscSFReduceBegin(), PetscSFSetGraph() 1468 @*/ 1469 PetscErrorCode PetscSFFetchAndOpBegin(PetscSF sf,MPI_Datatype unit,void *rootdata,const void *leafdata,void *leafupdate,MPI_Op op) 1470 { 1471 PetscErrorCode ierr; 1472 PetscMemType rootmtype,leafmtype,leafupdatemtype; 1473 1474 PetscFunctionBegin; 1475 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1476 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1477 ierr = PetscLogEventBegin(PETSCSF_FetchAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 1478 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1479 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1480 ierr = PetscGetMemType(leafupdate,&leafupdatemtype);CHKERRQ(ierr); 1481 if (leafmtype != leafupdatemtype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for leafdata and leafupdate in different memory types"); 1482 #if defined(PETSC_HAVE_CUDA) 1483 if (rootmtype == PETSC_MEMTYPE_DEVICE || leafmtype == PETSC_MEMTYPE_DEVICE) {cudaError_t err = cudaDeviceSynchronize();CHKERRCUDA(err);} 1484 #endif 1485 ierr = (*sf->ops->FetchAndOpBegin)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,leafupdate,op);CHKERRQ(ierr); 1486 ierr = PetscLogEventEnd(PETSCSF_FetchAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 1487 PetscFunctionReturn(0); 1488 } 1489 1490 /*@C 1491 PetscSFFetchAndOpEnd - end operation started in matching call to PetscSFFetchAndOpBegin() to fetch values from roots and update atomically by applying operation using my leaf value 1492 1493 Collective 1494 1495 Input Arguments: 1496 + sf - star forest 1497 . unit - data type 1498 . leafdata - leaf values to use in reduction 1499 - op - operation to use for reduction 1500 1501 Output Arguments: 1502 + rootdata - root values to be updated, input state is seen by first process to perform an update 1503 - leafupdate - state at each leaf's respective root immediately prior to my atomic update 1504 1505 Level: advanced 1506 1507 .seealso: PetscSFComputeDegreeEnd(), PetscSFReduceEnd(), PetscSFSetGraph() 1508 @*/ 1509 PetscErrorCode PetscSFFetchAndOpEnd(PetscSF sf,MPI_Datatype unit,void *rootdata,const void *leafdata,void *leafupdate,MPI_Op op) 1510 { 1511 PetscErrorCode ierr; 1512 PetscMemType rootmtype,leafmtype,leafupdatemtype; 1513 1514 PetscFunctionBegin; 1515 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1516 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1517 ierr = PetscLogEventBegin(PETSCSF_FetchAndOpEnd,sf,0,0,0);CHKERRQ(ierr); 1518 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1519 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1520 ierr = PetscGetMemType(leafupdate,&leafupdatemtype);CHKERRQ(ierr); 1521 if (leafmtype != leafupdatemtype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for leafdata and leafupdate in different memory types"); 1522 ierr = (*sf->ops->FetchAndOpEnd)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,leafupdate,op);CHKERRQ(ierr); 1523 ierr = PetscLogEventEnd(PETSCSF_FetchAndOpEnd,sf,0,0,0);CHKERRQ(ierr); 1524 PetscFunctionReturn(0); 1525 } 1526 1527 /*@C 1528 PetscSFComputeDegreeBegin - begin computation of degree for each root vertex, to be completed with PetscSFComputeDegreeEnd() 1529 1530 Collective 1531 1532 Input Arguments: 1533 . sf - star forest 1534 1535 Output Arguments: 1536 . degree - degree of each root vertex 1537 1538 Level: advanced 1539 1540 Notes: 1541 The returned array is owned by PetscSF and automatically freed by PetscSFDestroy(). Hence no need to call PetscFree() on it. 1542 1543 .seealso: PetscSFGatherBegin() 1544 @*/ 1545 PetscErrorCode PetscSFComputeDegreeBegin(PetscSF sf,const PetscInt **degree) 1546 { 1547 PetscErrorCode ierr; 1548 1549 PetscFunctionBegin; 1550 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1551 PetscSFCheckGraphSet(sf,1); 1552 PetscValidPointer(degree,2); 1553 if (!sf->degreeknown) { 1554 PetscInt i, nroots = sf->nroots, maxlocal = sf->maxleaf+1; /* TODO: We should use PetscSFGetLeafRange() */ 1555 if (sf->degree) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Calls to PetscSFComputeDegreeBegin() cannot be nested."); 1556 ierr = PetscMalloc1(nroots,&sf->degree);CHKERRQ(ierr); 1557 ierr = PetscMalloc1(PetscMax(maxlocal,1),&sf->degreetmp);CHKERRQ(ierr); /* allocate at least one entry, see check in PetscSFComputeDegreeEnd() */ 1558 for (i=0; i<nroots; i++) sf->degree[i] = 0; 1559 for (i=0; i<maxlocal; i++) sf->degreetmp[i] = 1; 1560 ierr = PetscSFReduceBegin(sf,MPIU_INT,sf->degreetmp,sf->degree,MPI_SUM);CHKERRQ(ierr); 1561 } 1562 *degree = NULL; 1563 PetscFunctionReturn(0); 1564 } 1565 1566 /*@C 1567 PetscSFComputeDegreeEnd - complete computation of degree for each root vertex, started with PetscSFComputeDegreeBegin() 1568 1569 Collective 1570 1571 Input Arguments: 1572 . sf - star forest 1573 1574 Output Arguments: 1575 . degree - degree of each root vertex 1576 1577 Level: developer 1578 1579 Notes: 1580 The returned array is owned by PetscSF and automatically freed by PetscSFDestroy(). Hence no need to call PetscFree() on it. 1581 1582 .seealso: 1583 @*/ 1584 PetscErrorCode PetscSFComputeDegreeEnd(PetscSF sf,const PetscInt **degree) 1585 { 1586 PetscErrorCode ierr; 1587 1588 PetscFunctionBegin; 1589 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1590 PetscSFCheckGraphSet(sf,1); 1591 PetscValidPointer(degree,2); 1592 if (!sf->degreeknown) { 1593 if (!sf->degreetmp) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Must call PetscSFComputeDegreeBegin() before PetscSFComputeDegreeEnd()"); 1594 ierr = PetscSFReduceEnd(sf,MPIU_INT,sf->degreetmp,sf->degree,MPI_SUM);CHKERRQ(ierr); 1595 ierr = PetscFree(sf->degreetmp);CHKERRQ(ierr); 1596 sf->degreeknown = PETSC_TRUE; 1597 } 1598 *degree = sf->degree; 1599 PetscFunctionReturn(0); 1600 } 1601 1602 1603 /*@C 1604 PetscSFComputeMultiRootOriginalNumbering - Returns original numbering of multi-roots (roots of multi-SF returned by PetscSFGetMultiSF()). 1605 Each multi-root is assigned index of the corresponding original root. 1606 1607 Collective 1608 1609 Input Arguments: 1610 + sf - star forest 1611 - degree - degree of each root vertex, computed with PetscSFComputeDegreeBegin()/PetscSFComputeDegreeEnd() 1612 1613 Output Arguments: 1614 + nMultiRoots - (optional) number of multi-roots (roots of multi-SF) 1615 - multiRootsOrigNumbering - original indices of multi-roots; length of this array is nMultiRoots 1616 1617 Level: developer 1618 1619 Notes: 1620 The returned array multiRootsOrigNumbering is newly allocated and should be destroyed with PetscFree() when no longer needed. 1621 1622 .seealso: PetscSFComputeDegreeBegin(), PetscSFComputeDegreeEnd(), PetscSFGetMultiSF() 1623 @*/ 1624 PetscErrorCode PetscSFComputeMultiRootOriginalNumbering(PetscSF sf, const PetscInt degree[], PetscInt *nMultiRoots, PetscInt *multiRootsOrigNumbering[]) 1625 { 1626 PetscSF msf; 1627 PetscInt i, j, k, nroots, nmroots; 1628 PetscErrorCode ierr; 1629 1630 PetscFunctionBegin; 1631 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1632 ierr = PetscSFGetGraph(sf, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 1633 if (nroots) PetscValidIntPointer(degree,2); 1634 if (nMultiRoots) PetscValidIntPointer(nMultiRoots,3); 1635 PetscValidPointer(multiRootsOrigNumbering,4); 1636 ierr = PetscSFGetMultiSF(sf,&msf);CHKERRQ(ierr); 1637 ierr = PetscSFGetGraph(msf, &nmroots, NULL, NULL, NULL);CHKERRQ(ierr); 1638 ierr = PetscMalloc1(nmroots, multiRootsOrigNumbering);CHKERRQ(ierr); 1639 for (i=0,j=0,k=0; i<nroots; i++) { 1640 if (!degree[i]) continue; 1641 for (j=0; j<degree[i]; j++,k++) { 1642 (*multiRootsOrigNumbering)[k] = i; 1643 } 1644 } 1645 #if defined(PETSC_USE_DEBUG) 1646 if (PetscUnlikely(k != nmroots)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sanity check fail"); 1647 #endif 1648 if (nMultiRoots) *nMultiRoots = nmroots; 1649 PetscFunctionReturn(0); 1650 } 1651 1652 /*@C 1653 PetscSFGatherBegin - begin pointwise gather of all leaves into multi-roots, to be completed with PetscSFGatherEnd() 1654 1655 Collective 1656 1657 Input Arguments: 1658 + sf - star forest 1659 . unit - data type 1660 - leafdata - leaf data to gather to roots 1661 1662 Output Argument: 1663 . multirootdata - root buffer to gather into, amount of space per root is equal to its degree 1664 1665 Level: intermediate 1666 1667 .seealso: PetscSFComputeDegreeBegin(), PetscSFScatterBegin() 1668 @*/ 1669 PetscErrorCode PetscSFGatherBegin(PetscSF sf,MPI_Datatype unit,const void *leafdata,void *multirootdata) 1670 { 1671 PetscErrorCode ierr; 1672 PetscSF multi; 1673 1674 PetscFunctionBegin; 1675 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1676 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1677 ierr = PetscSFGetMultiSF(sf,&multi);CHKERRQ(ierr); 1678 ierr = PetscSFReduceBegin(multi,unit,leafdata,multirootdata,MPIU_REPLACE);CHKERRQ(ierr); 1679 PetscFunctionReturn(0); 1680 } 1681 1682 /*@C 1683 PetscSFGatherEnd - ends pointwise gather operation that was started with PetscSFGatherBegin() 1684 1685 Collective 1686 1687 Input Arguments: 1688 + sf - star forest 1689 . unit - data type 1690 - leafdata - leaf data to gather to roots 1691 1692 Output Argument: 1693 . multirootdata - root buffer to gather into, amount of space per root is equal to its degree 1694 1695 Level: intermediate 1696 1697 .seealso: PetscSFComputeDegreeEnd(), PetscSFScatterEnd() 1698 @*/ 1699 PetscErrorCode PetscSFGatherEnd(PetscSF sf,MPI_Datatype unit,const void *leafdata,void *multirootdata) 1700 { 1701 PetscErrorCode ierr; 1702 PetscSF multi; 1703 1704 PetscFunctionBegin; 1705 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1706 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1707 ierr = PetscSFGetMultiSF(sf,&multi);CHKERRQ(ierr); 1708 ierr = PetscSFReduceEnd(multi,unit,leafdata,multirootdata,MPIU_REPLACE);CHKERRQ(ierr); 1709 PetscFunctionReturn(0); 1710 } 1711 1712 /*@C 1713 PetscSFScatterBegin - begin pointwise scatter operation from multi-roots to leaves, to be completed with PetscSFScatterEnd() 1714 1715 Collective 1716 1717 Input Arguments: 1718 + sf - star forest 1719 . unit - data type 1720 - multirootdata - root buffer to send to each leaf, one unit of data per leaf 1721 1722 Output Argument: 1723 . leafdata - leaf data to be update with personal data from each respective root 1724 1725 Level: intermediate 1726 1727 .seealso: PetscSFComputeDegreeBegin(), PetscSFScatterBegin() 1728 @*/ 1729 PetscErrorCode PetscSFScatterBegin(PetscSF sf,MPI_Datatype unit,const void *multirootdata,void *leafdata) 1730 { 1731 PetscErrorCode ierr; 1732 PetscSF multi; 1733 1734 PetscFunctionBegin; 1735 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1736 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1737 ierr = PetscSFGetMultiSF(sf,&multi);CHKERRQ(ierr); 1738 ierr = PetscSFBcastBegin(multi,unit,multirootdata,leafdata);CHKERRQ(ierr); 1739 PetscFunctionReturn(0); 1740 } 1741 1742 /*@C 1743 PetscSFScatterEnd - ends pointwise scatter operation that was started with PetscSFScatterBegin() 1744 1745 Collective 1746 1747 Input Arguments: 1748 + sf - star forest 1749 . unit - data type 1750 - multirootdata - root buffer to send to each leaf, one unit of data per leaf 1751 1752 Output Argument: 1753 . leafdata - leaf data to be update with personal data from each respective root 1754 1755 Level: intermediate 1756 1757 .seealso: PetscSFComputeDegreeEnd(), PetscSFScatterEnd() 1758 @*/ 1759 PetscErrorCode PetscSFScatterEnd(PetscSF sf,MPI_Datatype unit,const void *multirootdata,void *leafdata) 1760 { 1761 PetscErrorCode ierr; 1762 PetscSF multi; 1763 1764 PetscFunctionBegin; 1765 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1766 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1767 ierr = PetscSFGetMultiSF(sf,&multi);CHKERRQ(ierr); 1768 ierr = PetscSFBcastEnd(multi,unit,multirootdata,leafdata);CHKERRQ(ierr); 1769 PetscFunctionReturn(0); 1770 } 1771 1772 static PetscErrorCode PetscSFCheckLeavesUnique_Private(PetscSF sf) 1773 { 1774 #if defined(PETSC_USE_DEBUG) 1775 PetscInt i, n, nleaves; 1776 const PetscInt *ilocal = NULL; 1777 PetscHSetI seen; 1778 PetscErrorCode ierr; 1779 1780 PetscFunctionBegin; 1781 ierr = PetscSFGetGraph(sf,NULL,&nleaves,&ilocal,NULL);CHKERRQ(ierr); 1782 ierr = PetscHSetICreate(&seen);CHKERRQ(ierr); 1783 for (i = 0; i < nleaves; i++) { 1784 const PetscInt leaf = ilocal ? ilocal[i] : i; 1785 ierr = PetscHSetIAdd(seen,leaf);CHKERRQ(ierr); 1786 } 1787 ierr = PetscHSetIGetSize(seen,&n);CHKERRQ(ierr); 1788 if (n != nleaves) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Provided leaves have repeated values: all leaves must be unique"); 1789 ierr = PetscHSetIDestroy(&seen);CHKERRQ(ierr); 1790 PetscFunctionReturn(0); 1791 #else 1792 PetscFunctionBegin; 1793 PetscFunctionReturn(0); 1794 #endif 1795 } 1796 1797 /*@ 1798 PetscSFCompose - Compose a new PetscSF by putting the second SF under the first one in a top (roots) down (leaves) view 1799 1800 Input Parameters: 1801 + sfA - The first PetscSF 1802 - sfB - The second PetscSF 1803 1804 Output Parameters: 1805 . sfBA - The composite SF 1806 1807 Level: developer 1808 1809 Notes: 1810 Currently, the two SFs must be defined on congruent communicators and they must be true star 1811 forests, i.e. the same leaf is not connected with different roots. 1812 1813 sfA's leaf space and sfB's root space might be partially overlapped. The composition builds 1814 a graph with sfA's roots and sfB's leaves only when there is a path between them. Unconnected 1815 nodes (roots or leaves) are not in sfBA. Doing a Bcast on the new SF is equivalent to doing a 1816 Bcast on sfA, then a Bcast on sfB, on connected nodes. 1817 1818 .seealso: PetscSF, PetscSFComposeInverse(), PetscSFGetGraph(), PetscSFSetGraph() 1819 @*/ 1820 PetscErrorCode PetscSFCompose(PetscSF sfA,PetscSF sfB,PetscSF *sfBA) 1821 { 1822 PetscErrorCode ierr; 1823 const PetscSFNode *remotePointsA,*remotePointsB; 1824 PetscSFNode *remotePointsBA=NULL,*reorderedRemotePointsA = NULL,*leafdataB; 1825 const PetscInt *localPointsA,*localPointsB; 1826 PetscInt *localPointsBA; 1827 PetscInt i,numRootsA,numLeavesA,numRootsB,numLeavesB,minleaf,maxleaf,numLeavesBA; 1828 PetscBool denseB; 1829 1830 PetscFunctionBegin; 1831 PetscValidHeaderSpecific(sfA,PETSCSF_CLASSID,1); 1832 PetscSFCheckGraphSet(sfA,1); 1833 PetscValidHeaderSpecific(sfB,PETSCSF_CLASSID,2); 1834 PetscSFCheckGraphSet(sfB,2); 1835 PetscCheckSameComm(sfA,1,sfB,2); 1836 PetscValidPointer(sfBA,3); 1837 ierr = PetscSFCheckLeavesUnique_Private(sfA);CHKERRQ(ierr); 1838 ierr = PetscSFCheckLeavesUnique_Private(sfB);CHKERRQ(ierr); 1839 1840 ierr = PetscSFGetGraph(sfA,&numRootsA,&numLeavesA,&localPointsA,&remotePointsA);CHKERRQ(ierr); 1841 ierr = PetscSFGetGraph(sfB,&numRootsB,&numLeavesB,&localPointsB,&remotePointsB);CHKERRQ(ierr); 1842 if (localPointsA) { 1843 ierr = PetscMalloc1(numRootsB,&reorderedRemotePointsA);CHKERRQ(ierr); 1844 for (i=0; i<numRootsB; i++) { 1845 reorderedRemotePointsA[i].rank = -1; 1846 reorderedRemotePointsA[i].index = -1; 1847 } 1848 for (i=0; i<numLeavesA; i++) { 1849 if (localPointsA[i] >= numRootsB) continue; 1850 reorderedRemotePointsA[localPointsA[i]] = remotePointsA[i]; 1851 } 1852 remotePointsA = reorderedRemotePointsA; 1853 } 1854 ierr = PetscSFGetLeafRange(sfB,&minleaf,&maxleaf);CHKERRQ(ierr); 1855 ierr = PetscMalloc1(maxleaf-minleaf+1,&leafdataB);CHKERRQ(ierr); 1856 ierr = PetscSFBcastBegin(sfB,MPIU_2INT,remotePointsA,leafdataB-minleaf);CHKERRQ(ierr); 1857 ierr = PetscSFBcastEnd(sfB,MPIU_2INT,remotePointsA,leafdataB-minleaf);CHKERRQ(ierr); 1858 ierr = PetscFree(reorderedRemotePointsA);CHKERRQ(ierr); 1859 1860 denseB = (PetscBool)!localPointsB; 1861 for (i=0,numLeavesBA=0; i<numLeavesB; i++) { 1862 if (leafdataB[localPointsB ? localPointsB[i]-minleaf : i].rank == -1) denseB = PETSC_FALSE; 1863 else numLeavesBA++; 1864 } 1865 if (denseB) { 1866 localPointsBA = NULL; 1867 remotePointsBA = leafdataB; 1868 } else { 1869 ierr = PetscMalloc1(numLeavesBA,&localPointsBA);CHKERRQ(ierr); 1870 ierr = PetscMalloc1(numLeavesBA,&remotePointsBA);CHKERRQ(ierr); 1871 for (i=0,numLeavesBA=0; i<numLeavesB; i++) { 1872 const PetscInt l = localPointsB ? localPointsB[i] : i; 1873 1874 if (leafdataB[l-minleaf].rank == -1) continue; 1875 remotePointsBA[numLeavesBA] = leafdataB[l-minleaf]; 1876 localPointsBA[numLeavesBA] = l; 1877 numLeavesBA++; 1878 } 1879 ierr = PetscFree(leafdataB);CHKERRQ(ierr); 1880 } 1881 ierr = PetscSFCreate(PetscObjectComm((PetscObject)sfA),sfBA);CHKERRQ(ierr); 1882 ierr = PetscSFSetGraph(*sfBA,numRootsA,numLeavesBA,localPointsBA,PETSC_OWN_POINTER,remotePointsBA,PETSC_OWN_POINTER);CHKERRQ(ierr); 1883 PetscFunctionReturn(0); 1884 } 1885 1886 /*@ 1887 PetscSFComposeInverse - Compose a new PetscSF by putting the inverse of the second SF under the first one 1888 1889 Input Parameters: 1890 + sfA - The first PetscSF 1891 - sfB - The second PetscSF 1892 1893 Output Parameters: 1894 . sfBA - The composite SF. 1895 1896 Level: developer 1897 1898 Notes: 1899 Currently, the two SFs must be defined on congruent communicators and they must be true star 1900 forests, i.e. the same leaf is not connected with different roots. Even more, all roots of the 1901 second SF must have a degree of 1, i.e., no roots have more than one leaf connected. 1902 1903 sfA's leaf space and sfB's leaf space might be partially overlapped. The composition builds 1904 a graph with sfA's roots and sfB's roots only when there is a path between them. Unconnected 1905 roots are not in sfBA. Doing a Bcast on the new SF is equivalent to doing a Bcast on sfA, then 1906 a Reduce on sfB, on connected roots. 1907 1908 .seealso: PetscSF, PetscSFCompose(), PetscSFGetGraph(), PetscSFSetGraph(), PetscSFCreateInverseSF() 1909 @*/ 1910 PetscErrorCode PetscSFComposeInverse(PetscSF sfA,PetscSF sfB,PetscSF *sfBA) 1911 { 1912 PetscErrorCode ierr; 1913 const PetscSFNode *remotePointsA,*remotePointsB; 1914 PetscSFNode *remotePointsBA; 1915 const PetscInt *localPointsA,*localPointsB; 1916 PetscSFNode *reorderedRemotePointsA = NULL; 1917 PetscInt i,numRootsA,numLeavesA,numLeavesBA,numRootsB,numLeavesB,minleaf,maxleaf,*localPointsBA; 1918 1919 PetscFunctionBegin; 1920 PetscValidHeaderSpecific(sfA,PETSCSF_CLASSID,1); 1921 PetscSFCheckGraphSet(sfA,1); 1922 PetscValidHeaderSpecific(sfB,PETSCSF_CLASSID,2); 1923 PetscSFCheckGraphSet(sfB,2); 1924 PetscCheckSameComm(sfA,1,sfB,2); 1925 PetscValidPointer(sfBA,3); 1926 ierr = PetscSFCheckLeavesUnique_Private(sfA);CHKERRQ(ierr); 1927 ierr = PetscSFCheckLeavesUnique_Private(sfB);CHKERRQ(ierr); 1928 /* TODO: Check roots of sfB have degree of 1 */ 1929 1930 ierr = PetscSFGetGraph(sfA, &numRootsA, &numLeavesA, &localPointsA, &remotePointsA);CHKERRQ(ierr); 1931 ierr = PetscSFGetGraph(sfB, &numRootsB, &numLeavesB, &localPointsB, &remotePointsB);CHKERRQ(ierr); 1932 ierr = PetscSFGetLeafRange(sfB, &minleaf, &maxleaf);CHKERRQ(ierr); 1933 ierr = PetscMalloc1(maxleaf - minleaf + 1,&reorderedRemotePointsA);CHKERRQ(ierr); 1934 for (i=0; i<maxleaf - minleaf + 1; i++) { 1935 reorderedRemotePointsA[i].rank = -1; 1936 reorderedRemotePointsA[i].index = -1; 1937 } 1938 if (localPointsA) { 1939 for (i=0; i<numLeavesA; i++) { 1940 if (localPointsA[i] > maxleaf || localPointsA[i] < minleaf) continue; 1941 reorderedRemotePointsA[localPointsA[i] - minleaf] = remotePointsA[i]; 1942 } 1943 } else { 1944 for (i=0; i<numLeavesA; i++) { 1945 if (i > maxleaf || i < minleaf) continue; 1946 reorderedRemotePointsA[i - minleaf] = remotePointsA[i]; 1947 } 1948 } 1949 1950 ierr = PetscMalloc1(numRootsB,&localPointsBA);CHKERRQ(ierr); 1951 ierr = PetscMalloc1(numRootsB,&remotePointsBA);CHKERRQ(ierr); 1952 for (i=0; i<numRootsB; i++) { 1953 remotePointsBA[i].rank = -1; 1954 remotePointsBA[i].index = -1; 1955 } 1956 1957 /* Once we implement the TODO above (check all roots of sfB have degree of 1), we can replace the MPI_MAXLOC 1958 with MPIU_REPLACE. In that case, MPI_MAXLOC and MPIU_REPLACE have the same effect. 1959 */ 1960 ierr = PetscSFReduceBegin(sfB,MPIU_2INT,reorderedRemotePointsA-minleaf,remotePointsBA,MPI_MAXLOC);CHKERRQ(ierr); 1961 ierr = PetscSFReduceEnd(sfB,MPIU_2INT,reorderedRemotePointsA-minleaf,remotePointsBA,MPI_MAXLOC);CHKERRQ(ierr); 1962 ierr = PetscFree(reorderedRemotePointsA);CHKERRQ(ierr); 1963 for (i=0,numLeavesBA=0; i<numRootsB; i++) { 1964 if (remotePointsBA[i].rank == -1) continue; 1965 remotePointsBA[numLeavesBA].rank = remotePointsBA[i].rank; 1966 remotePointsBA[numLeavesBA].index = remotePointsBA[i].index; 1967 localPointsBA[numLeavesBA] = i; 1968 numLeavesBA++; 1969 } 1970 ierr = PetscSFCreate(PetscObjectComm((PetscObject)sfA),sfBA);CHKERRQ(ierr); 1971 ierr = PetscSFSetGraph(*sfBA,numRootsA,numLeavesBA,localPointsBA,PETSC_OWN_POINTER,remotePointsBA,PETSC_OWN_POINTER);CHKERRQ(ierr); 1972 PetscFunctionReturn(0); 1973 } 1974 1975 /* 1976 PetscSFCreateLocalSF_Private - Creates a local PetscSF that only has intra-process edges of the global PetscSF 1977 1978 Input Parameters: 1979 . sf - The global PetscSF 1980 1981 Output Parameters: 1982 . out - The local PetscSF 1983 */ 1984 PetscErrorCode PetscSFCreateLocalSF_Private(PetscSF sf,PetscSF *out) 1985 { 1986 MPI_Comm comm; 1987 PetscMPIInt myrank; 1988 const PetscInt *ilocal; 1989 const PetscSFNode *iremote; 1990 PetscInt i,j,nroots,nleaves,lnleaves,*lilocal; 1991 PetscSFNode *liremote; 1992 PetscSF lsf; 1993 PetscErrorCode ierr; 1994 1995 PetscFunctionBegin; 1996 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1997 if (sf->ops->CreateLocalSF) { 1998 ierr = (*sf->ops->CreateLocalSF)(sf,out);CHKERRQ(ierr); 1999 } else { 2000 /* Could use PetscSFCreateEmbeddedLeafSF, but since we know the comm is PETSC_COMM_SELF, we can make it fast */ 2001 ierr = PetscObjectGetComm((PetscObject)sf,&comm);CHKERRQ(ierr); 2002 ierr = MPI_Comm_rank(comm,&myrank);CHKERRQ(ierr); 2003 2004 /* Find out local edges and build a local SF */ 2005 ierr = PetscSFGetGraph(sf,&nroots,&nleaves,&ilocal,&iremote);CHKERRQ(ierr); 2006 for (i=lnleaves=0; i<nleaves; i++) {if (iremote[i].rank == (PetscInt)myrank) lnleaves++;} 2007 ierr = PetscMalloc1(lnleaves,&lilocal);CHKERRQ(ierr); 2008 ierr = PetscMalloc1(lnleaves,&liremote);CHKERRQ(ierr); 2009 2010 for (i=j=0; i<nleaves; i++) { 2011 if (iremote[i].rank == (PetscInt)myrank) { 2012 lilocal[j] = ilocal? ilocal[i] : i; /* ilocal=NULL for contiguous storage */ 2013 liremote[j].rank = 0; /* rank in PETSC_COMM_SELF */ 2014 liremote[j].index = iremote[i].index; 2015 j++; 2016 } 2017 } 2018 ierr = PetscSFCreate(PETSC_COMM_SELF,&lsf);CHKERRQ(ierr); 2019 ierr = PetscSFSetGraph(lsf,nroots,lnleaves,lilocal,PETSC_OWN_POINTER,liremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 2020 ierr = PetscSFSetUp(lsf);CHKERRQ(ierr); 2021 *out = lsf; 2022 } 2023 PetscFunctionReturn(0); 2024 } 2025 2026 /* Similar to PetscSFBcast, but only Bcast to leaves on rank 0 */ 2027 PetscErrorCode PetscSFBcastToZero_Private(PetscSF sf,MPI_Datatype unit,const void *rootdata,void *leafdata) 2028 { 2029 PetscErrorCode ierr; 2030 PetscMemType rootmtype,leafmtype; 2031 2032 PetscFunctionBegin; 2033 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 2034 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 2035 ierr = PetscLogEventBegin(PETSCSF_BcastAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 2036 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 2037 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 2038 if (sf->ops->BcastToZero) { 2039 ierr = (*sf->ops->BcastToZero)(sf,unit,rootmtype,rootdata,leafmtype,leafdata);CHKERRQ(ierr); 2040 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"PetscSFBcastToZero_Private is not supported on this SF type"); 2041 ierr = PetscLogEventEnd(PETSCSF_BcastAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 2042 PetscFunctionReturn(0); 2043 } 2044 2045