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 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 PetscFunctionReturn(0); 1231 } 1232 1233 /*@C 1234 PetscSFCreateEmbeddedLeafSF - removes edges from all but the selected leaves, does not remap indices 1235 1236 Collective 1237 1238 Input Arguments: 1239 + sf - original star forest 1240 . nselected - number of selected leaves on this process 1241 - selected - indices of the selected leaves on this process 1242 1243 Output Arguments: 1244 . newsf - new star forest 1245 1246 Level: advanced 1247 1248 .seealso: PetscSFCreateEmbeddedSF(), PetscSFSetGraph(), PetscSFGetGraph() 1249 @*/ 1250 PetscErrorCode PetscSFCreateEmbeddedLeafSF(PetscSF sf,PetscInt nselected,const PetscInt *selected,PetscSF *newsf) 1251 { 1252 const PetscSFNode *iremote; 1253 PetscSFNode *new_iremote; 1254 const PetscInt *ilocal; 1255 PetscInt i,nroots,*leaves,*new_ilocal; 1256 MPI_Comm comm; 1257 PetscErrorCode ierr; 1258 1259 PetscFunctionBegin; 1260 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1261 PetscSFCheckGraphSet(sf,1); 1262 if (nselected) PetscValidPointer(selected,3); 1263 PetscValidPointer(newsf,4); 1264 1265 /* Uniq selected[] and put results in leaves[] */ 1266 ierr = PetscObjectGetComm((PetscObject)sf,&comm);CHKERRQ(ierr); 1267 ierr = PetscMalloc1(nselected,&leaves);CHKERRQ(ierr); 1268 ierr = PetscArraycpy(leaves,selected,nselected);CHKERRQ(ierr); 1269 ierr = PetscSortedRemoveDupsInt(&nselected,leaves);CHKERRQ(ierr); 1270 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); 1271 1272 /* Optimize the routine only when sf is setup and hence we can reuse sf's communication pattern */ 1273 if (sf->setupcalled && sf->ops->CreateEmbeddedLeafSF) { 1274 ierr = (*sf->ops->CreateEmbeddedLeafSF)(sf,nselected,leaves,newsf);CHKERRQ(ierr); 1275 } else { 1276 ierr = PetscSFGetGraph(sf,&nroots,NULL,&ilocal,&iremote);CHKERRQ(ierr); 1277 ierr = PetscMalloc1(nselected,&new_ilocal);CHKERRQ(ierr); 1278 ierr = PetscMalloc1(nselected,&new_iremote);CHKERRQ(ierr); 1279 for (i=0; i<nselected; ++i) { 1280 const PetscInt l = leaves[i]; 1281 new_ilocal[i] = ilocal ? ilocal[l] : l; 1282 new_iremote[i].rank = iremote[l].rank; 1283 new_iremote[i].index = iremote[l].index; 1284 } 1285 ierr = PetscSFCreate(comm,newsf);CHKERRQ(ierr); 1286 ierr = PetscSFSetFromOptions(*newsf);CHKERRQ(ierr); 1287 ierr = PetscSFSetGraph(*newsf,nroots,nselected,new_ilocal,PETSC_OWN_POINTER,new_iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1288 } 1289 ierr = PetscFree(leaves);CHKERRQ(ierr); 1290 PetscFunctionReturn(0); 1291 } 1292 1293 /*@C 1294 PetscSFBcastAndOpBegin - begin pointwise broadcast with root value being reduced to leaf value, to be concluded with call to PetscSFBcastAndOpEnd() 1295 1296 Collective on PetscSF 1297 1298 Input Arguments: 1299 + sf - star forest on which to communicate 1300 . unit - data type associated with each node 1301 . rootdata - buffer to broadcast 1302 - op - operation to use for reduction 1303 1304 Output Arguments: 1305 . leafdata - buffer to be reduced with values from each leaf's respective root 1306 1307 Level: intermediate 1308 1309 .seealso: PetscSFBcastAndOpEnd(), PetscSFBcastBegin(), PetscSFBcastEnd() 1310 @*/ 1311 PetscErrorCode PetscSFBcastAndOpBegin(PetscSF sf,MPI_Datatype unit,const void *rootdata,void *leafdata,MPI_Op op) 1312 { 1313 PetscErrorCode ierr; 1314 PetscMemType rootmtype,leafmtype; 1315 1316 PetscFunctionBegin; 1317 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1318 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1319 ierr = PetscLogEventBegin(PETSCSF_BcastAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 1320 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1321 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1322 #if defined(PETSC_HAVE_CUDA) 1323 /* Shall we assume rootdata, leafdata are ready to use (instead of being computed by some asynchronous kernels)? 1324 To be similar to MPI, I'd like to have this assumption, since MPI does not have a concept of stream. 1325 But currently this assumption is not enforecd in Petsc. To be safe, I do synchronization here. Otherwise, if 1326 we do not sync now and call the Pack kernel directly on the default NULL stream (assume petsc objects are also 1327 computed on it), we have to sync the NULL stream before calling MPI routines. So, it looks a cudaDeviceSynchronize 1328 is inevitable. We do it now and put pack/unpack kernels to non-NULL streams. 1329 */ 1330 if (rootmtype == PETSC_MEMTYPE_DEVICE || leafmtype == PETSC_MEMTYPE_DEVICE) {cudaError_t err = cudaDeviceSynchronize();CHKERRCUDA(err);} 1331 #endif 1332 ierr = (*sf->ops->BcastAndOpBegin)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,op);CHKERRQ(ierr); 1333 ierr = PetscLogEventEnd(PETSCSF_BcastAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 1334 PetscFunctionReturn(0); 1335 } 1336 1337 /*@C 1338 PetscSFBcastAndOpEnd - end a broadcast & reduce operation started with PetscSFBcastAndOpBegin() 1339 1340 Collective 1341 1342 Input Arguments: 1343 + sf - star forest 1344 . unit - data type 1345 . rootdata - buffer to broadcast 1346 - op - operation to use for reduction 1347 1348 Output Arguments: 1349 . leafdata - buffer to be reduced with values from each leaf's respective root 1350 1351 Level: intermediate 1352 1353 .seealso: PetscSFSetGraph(), PetscSFReduceEnd() 1354 @*/ 1355 PetscErrorCode PetscSFBcastAndOpEnd(PetscSF sf,MPI_Datatype unit,const void *rootdata,void *leafdata,MPI_Op op) 1356 { 1357 PetscErrorCode ierr; 1358 PetscMemType rootmtype,leafmtype; 1359 1360 PetscFunctionBegin; 1361 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1362 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1363 ierr = PetscLogEventBegin(PETSCSF_BcastAndOpEnd,sf,0,0,0);CHKERRQ(ierr); 1364 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1365 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1366 ierr = (*sf->ops->BcastAndOpEnd)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,op);CHKERRQ(ierr); 1367 ierr = PetscLogEventEnd(PETSCSF_BcastAndOpEnd,sf,0,0,0);CHKERRQ(ierr); 1368 PetscFunctionReturn(0); 1369 } 1370 1371 /*@C 1372 PetscSFReduceBegin - begin reduction of leafdata into rootdata, to be completed with call to PetscSFReduceEnd() 1373 1374 Collective 1375 1376 Input Arguments: 1377 + sf - star forest 1378 . unit - data type 1379 . leafdata - values to reduce 1380 - op - reduction operation 1381 1382 Output Arguments: 1383 . rootdata - result of reduction of values from all leaves of each root 1384 1385 Level: intermediate 1386 1387 .seealso: PetscSFBcastBegin() 1388 @*/ 1389 PetscErrorCode PetscSFReduceBegin(PetscSF sf,MPI_Datatype unit,const void *leafdata,void *rootdata,MPI_Op op) 1390 { 1391 PetscErrorCode ierr; 1392 PetscMemType rootmtype,leafmtype; 1393 1394 PetscFunctionBegin; 1395 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1396 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1397 ierr = PetscLogEventBegin(PETSCSF_ReduceBegin,sf,0,0,0);CHKERRQ(ierr); 1398 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1399 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1400 #if defined(PETSC_HAVE_CUDA) 1401 if (rootmtype == PETSC_MEMTYPE_DEVICE || leafmtype == PETSC_MEMTYPE_DEVICE) {cudaError_t err = cudaDeviceSynchronize();CHKERRCUDA(err);} 1402 #endif 1403 ierr = (sf->ops->ReduceBegin)(sf,unit,leafmtype,leafdata,rootmtype,rootdata,op);CHKERRQ(ierr); 1404 ierr = PetscLogEventEnd(PETSCSF_ReduceBegin,sf,0,0,0);CHKERRQ(ierr); 1405 PetscFunctionReturn(0); 1406 } 1407 1408 /*@C 1409 PetscSFReduceEnd - end a reduction operation started with PetscSFReduceBegin() 1410 1411 Collective 1412 1413 Input Arguments: 1414 + sf - star forest 1415 . unit - data type 1416 . leafdata - values to reduce 1417 - op - reduction operation 1418 1419 Output Arguments: 1420 . rootdata - result of reduction of values from all leaves of each root 1421 1422 Level: intermediate 1423 1424 .seealso: PetscSFSetGraph(), PetscSFBcastEnd() 1425 @*/ 1426 PetscErrorCode PetscSFReduceEnd(PetscSF sf,MPI_Datatype unit,const void *leafdata,void *rootdata,MPI_Op op) 1427 { 1428 PetscErrorCode ierr; 1429 PetscMemType rootmtype,leafmtype; 1430 1431 PetscFunctionBegin; 1432 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1433 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1434 ierr = PetscLogEventBegin(PETSCSF_ReduceEnd,sf,0,0,0);CHKERRQ(ierr); 1435 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1436 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1437 ierr = (*sf->ops->ReduceEnd)(sf,unit,leafmtype,leafdata,rootmtype,rootdata,op);CHKERRQ(ierr); 1438 ierr = PetscLogEventEnd(PETSCSF_ReduceEnd,sf,0,0,0);CHKERRQ(ierr); 1439 PetscFunctionReturn(0); 1440 } 1441 1442 /*@C 1443 PetscSFFetchAndOpBegin - begin operation that fetches values from root and updates atomically by applying operation using my leaf value, to be completed with PetscSFFetchAndOpEnd() 1444 1445 Collective 1446 1447 Input Arguments: 1448 + sf - star forest 1449 . unit - data type 1450 . leafdata - leaf values to use in reduction 1451 - op - operation to use for reduction 1452 1453 Output Arguments: 1454 + rootdata - root values to be updated, input state is seen by first process to perform an update 1455 - leafupdate - state at each leaf's respective root immediately prior to my atomic update 1456 1457 Level: advanced 1458 1459 Note: 1460 The update is only atomic at the granularity provided by the hardware. Different roots referenced by the same process 1461 might be updated in a different order. Furthermore, if a composite type is used for the unit datatype, atomicity is 1462 not guaranteed across the whole vertex. Therefore, this function is mostly only used with primitive types such as 1463 integers. 1464 1465 .seealso: PetscSFComputeDegreeBegin(), PetscSFReduceBegin(), PetscSFSetGraph() 1466 @*/ 1467 PetscErrorCode PetscSFFetchAndOpBegin(PetscSF sf,MPI_Datatype unit,void *rootdata,const void *leafdata,void *leafupdate,MPI_Op op) 1468 { 1469 PetscErrorCode ierr; 1470 PetscMemType rootmtype,leafmtype,leafupdatemtype; 1471 1472 PetscFunctionBegin; 1473 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1474 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1475 ierr = PetscLogEventBegin(PETSCSF_FetchAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 1476 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1477 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1478 ierr = PetscGetMemType(leafupdate,&leafupdatemtype);CHKERRQ(ierr); 1479 if (leafmtype != leafupdatemtype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for leafdata and leafupdate in different memory types"); 1480 #if defined(PETSC_HAVE_CUDA) 1481 if (rootmtype == PETSC_MEMTYPE_DEVICE || leafmtype == PETSC_MEMTYPE_DEVICE) {cudaError_t err = cudaDeviceSynchronize();CHKERRCUDA(err);} 1482 #endif 1483 ierr = (*sf->ops->FetchAndOpBegin)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,leafupdate,op);CHKERRQ(ierr); 1484 ierr = PetscLogEventEnd(PETSCSF_FetchAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 1485 PetscFunctionReturn(0); 1486 } 1487 1488 /*@C 1489 PetscSFFetchAndOpEnd - end operation started in matching call to PetscSFFetchAndOpBegin() to fetch values from roots and update atomically by applying operation using my leaf value 1490 1491 Collective 1492 1493 Input Arguments: 1494 + sf - star forest 1495 . unit - data type 1496 . leafdata - leaf values to use in reduction 1497 - op - operation to use for reduction 1498 1499 Output Arguments: 1500 + rootdata - root values to be updated, input state is seen by first process to perform an update 1501 - leafupdate - state at each leaf's respective root immediately prior to my atomic update 1502 1503 Level: advanced 1504 1505 .seealso: PetscSFComputeDegreeEnd(), PetscSFReduceEnd(), PetscSFSetGraph() 1506 @*/ 1507 PetscErrorCode PetscSFFetchAndOpEnd(PetscSF sf,MPI_Datatype unit,void *rootdata,const void *leafdata,void *leafupdate,MPI_Op op) 1508 { 1509 PetscErrorCode ierr; 1510 PetscMemType rootmtype,leafmtype,leafupdatemtype; 1511 1512 PetscFunctionBegin; 1513 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1514 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1515 ierr = PetscLogEventBegin(PETSCSF_FetchAndOpEnd,sf,0,0,0);CHKERRQ(ierr); 1516 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 1517 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 1518 ierr = PetscGetMemType(leafupdate,&leafupdatemtype);CHKERRQ(ierr); 1519 if (leafmtype != leafupdatemtype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for leafdata and leafupdate in different memory types"); 1520 ierr = (*sf->ops->FetchAndOpEnd)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,leafupdate,op);CHKERRQ(ierr); 1521 ierr = PetscLogEventEnd(PETSCSF_FetchAndOpEnd,sf,0,0,0);CHKERRQ(ierr); 1522 PetscFunctionReturn(0); 1523 } 1524 1525 /*@C 1526 PetscSFComputeDegreeBegin - begin computation of degree for each root vertex, to be completed with PetscSFComputeDegreeEnd() 1527 1528 Collective 1529 1530 Input Arguments: 1531 . sf - star forest 1532 1533 Output Arguments: 1534 . degree - degree of each root vertex 1535 1536 Level: advanced 1537 1538 Notes: 1539 The returned array is owned by PetscSF and automatically freed by PetscSFDestroy(). Hence no need to call PetscFree() on it. 1540 1541 .seealso: PetscSFGatherBegin() 1542 @*/ 1543 PetscErrorCode PetscSFComputeDegreeBegin(PetscSF sf,const PetscInt **degree) 1544 { 1545 PetscErrorCode ierr; 1546 1547 PetscFunctionBegin; 1548 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1549 PetscSFCheckGraphSet(sf,1); 1550 PetscValidPointer(degree,2); 1551 if (!sf->degreeknown) { 1552 PetscInt i, nroots = sf->nroots, maxlocal = sf->maxleaf+1; /* TODO: We should use PetscSFGetLeafRange() */ 1553 if (sf->degree) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Calls to PetscSFComputeDegreeBegin() cannot be nested."); 1554 ierr = PetscMalloc1(nroots,&sf->degree);CHKERRQ(ierr); 1555 ierr = PetscMalloc1(PetscMax(maxlocal,1),&sf->degreetmp);CHKERRQ(ierr); /* allocate at least one entry, see check in PetscSFComputeDegreeEnd() */ 1556 for (i=0; i<nroots; i++) sf->degree[i] = 0; 1557 for (i=0; i<maxlocal; i++) sf->degreetmp[i] = 1; 1558 ierr = PetscSFReduceBegin(sf,MPIU_INT,sf->degreetmp,sf->degree,MPI_SUM);CHKERRQ(ierr); 1559 } 1560 *degree = NULL; 1561 PetscFunctionReturn(0); 1562 } 1563 1564 /*@C 1565 PetscSFComputeDegreeEnd - complete computation of degree for each root vertex, started with PetscSFComputeDegreeBegin() 1566 1567 Collective 1568 1569 Input Arguments: 1570 . sf - star forest 1571 1572 Output Arguments: 1573 . degree - degree of each root vertex 1574 1575 Level: developer 1576 1577 Notes: 1578 The returned array is owned by PetscSF and automatically freed by PetscSFDestroy(). Hence no need to call PetscFree() on it. 1579 1580 .seealso: 1581 @*/ 1582 PetscErrorCode PetscSFComputeDegreeEnd(PetscSF sf,const PetscInt **degree) 1583 { 1584 PetscErrorCode ierr; 1585 1586 PetscFunctionBegin; 1587 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1588 PetscSFCheckGraphSet(sf,1); 1589 PetscValidPointer(degree,2); 1590 if (!sf->degreeknown) { 1591 if (!sf->degreetmp) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Must call PetscSFComputeDegreeBegin() before PetscSFComputeDegreeEnd()"); 1592 ierr = PetscSFReduceEnd(sf,MPIU_INT,sf->degreetmp,sf->degree,MPI_SUM);CHKERRQ(ierr); 1593 ierr = PetscFree(sf->degreetmp);CHKERRQ(ierr); 1594 sf->degreeknown = PETSC_TRUE; 1595 } 1596 *degree = sf->degree; 1597 PetscFunctionReturn(0); 1598 } 1599 1600 1601 /*@C 1602 PetscSFComputeMultiRootOriginalNumbering - Returns original numbering of multi-roots (roots of multi-SF returned by PetscSFGetMultiSF()). 1603 Each multi-root is assigned index of the corresponding original root. 1604 1605 Collective 1606 1607 Input Arguments: 1608 + sf - star forest 1609 - degree - degree of each root vertex, computed with PetscSFComputeDegreeBegin()/PetscSFComputeDegreeEnd() 1610 1611 Output Arguments: 1612 + nMultiRoots - (optional) number of multi-roots (roots of multi-SF) 1613 - multiRootsOrigNumbering - original indices of multi-roots; length of this array is nMultiRoots 1614 1615 Level: developer 1616 1617 Notes: 1618 The returned array multiRootsOrigNumbering is newly allocated and should be destroyed with PetscFree() when no longer needed. 1619 1620 .seealso: PetscSFComputeDegreeBegin(), PetscSFComputeDegreeEnd(), PetscSFGetMultiSF() 1621 @*/ 1622 PetscErrorCode PetscSFComputeMultiRootOriginalNumbering(PetscSF sf, const PetscInt degree[], PetscInt *nMultiRoots, PetscInt *multiRootsOrigNumbering[]) 1623 { 1624 PetscSF msf; 1625 PetscInt i, j, k, nroots, nmroots; 1626 PetscErrorCode ierr; 1627 1628 PetscFunctionBegin; 1629 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1630 ierr = PetscSFGetGraph(sf, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 1631 if (nroots) PetscValidIntPointer(degree,2); 1632 if (nMultiRoots) PetscValidIntPointer(nMultiRoots,3); 1633 PetscValidPointer(multiRootsOrigNumbering,4); 1634 ierr = PetscSFGetMultiSF(sf,&msf);CHKERRQ(ierr); 1635 ierr = PetscSFGetGraph(msf, &nmroots, NULL, NULL, NULL);CHKERRQ(ierr); 1636 ierr = PetscMalloc1(nmroots, multiRootsOrigNumbering);CHKERRQ(ierr); 1637 for (i=0,j=0,k=0; i<nroots; i++) { 1638 if (!degree[i]) continue; 1639 for (j=0; j<degree[i]; j++,k++) { 1640 (*multiRootsOrigNumbering)[k] = i; 1641 } 1642 } 1643 #if defined(PETSC_USE_DEBUG) 1644 if (PetscUnlikely(k != nmroots)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sanity check fail"); 1645 #endif 1646 if (nMultiRoots) *nMultiRoots = nmroots; 1647 PetscFunctionReturn(0); 1648 } 1649 1650 /*@C 1651 PetscSFGatherBegin - begin pointwise gather of all leaves into multi-roots, to be completed with PetscSFGatherEnd() 1652 1653 Collective 1654 1655 Input Arguments: 1656 + sf - star forest 1657 . unit - data type 1658 - leafdata - leaf data to gather to roots 1659 1660 Output Argument: 1661 . multirootdata - root buffer to gather into, amount of space per root is equal to its degree 1662 1663 Level: intermediate 1664 1665 .seealso: PetscSFComputeDegreeBegin(), PetscSFScatterBegin() 1666 @*/ 1667 PetscErrorCode PetscSFGatherBegin(PetscSF sf,MPI_Datatype unit,const void *leafdata,void *multirootdata) 1668 { 1669 PetscErrorCode ierr; 1670 PetscSF multi; 1671 1672 PetscFunctionBegin; 1673 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1674 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1675 ierr = PetscSFGetMultiSF(sf,&multi);CHKERRQ(ierr); 1676 ierr = PetscSFReduceBegin(multi,unit,leafdata,multirootdata,MPIU_REPLACE);CHKERRQ(ierr); 1677 PetscFunctionReturn(0); 1678 } 1679 1680 /*@C 1681 PetscSFGatherEnd - ends pointwise gather operation that was started with PetscSFGatherBegin() 1682 1683 Collective 1684 1685 Input Arguments: 1686 + sf - star forest 1687 . unit - data type 1688 - leafdata - leaf data to gather to roots 1689 1690 Output Argument: 1691 . multirootdata - root buffer to gather into, amount of space per root is equal to its degree 1692 1693 Level: intermediate 1694 1695 .seealso: PetscSFComputeDegreeEnd(), PetscSFScatterEnd() 1696 @*/ 1697 PetscErrorCode PetscSFGatherEnd(PetscSF sf,MPI_Datatype unit,const void *leafdata,void *multirootdata) 1698 { 1699 PetscErrorCode ierr; 1700 PetscSF multi; 1701 1702 PetscFunctionBegin; 1703 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1704 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1705 ierr = PetscSFGetMultiSF(sf,&multi);CHKERRQ(ierr); 1706 ierr = PetscSFReduceEnd(multi,unit,leafdata,multirootdata,MPIU_REPLACE);CHKERRQ(ierr); 1707 PetscFunctionReturn(0); 1708 } 1709 1710 /*@C 1711 PetscSFScatterBegin - begin pointwise scatter operation from multi-roots to leaves, to be completed with PetscSFScatterEnd() 1712 1713 Collective 1714 1715 Input Arguments: 1716 + sf - star forest 1717 . unit - data type 1718 - multirootdata - root buffer to send to each leaf, one unit of data per leaf 1719 1720 Output Argument: 1721 . leafdata - leaf data to be update with personal data from each respective root 1722 1723 Level: intermediate 1724 1725 .seealso: PetscSFComputeDegreeBegin(), PetscSFScatterBegin() 1726 @*/ 1727 PetscErrorCode PetscSFScatterBegin(PetscSF sf,MPI_Datatype unit,const void *multirootdata,void *leafdata) 1728 { 1729 PetscErrorCode ierr; 1730 PetscSF multi; 1731 1732 PetscFunctionBegin; 1733 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1734 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1735 ierr = PetscSFGetMultiSF(sf,&multi);CHKERRQ(ierr); 1736 ierr = PetscSFBcastBegin(multi,unit,multirootdata,leafdata);CHKERRQ(ierr); 1737 PetscFunctionReturn(0); 1738 } 1739 1740 /*@C 1741 PetscSFScatterEnd - ends pointwise scatter operation that was started with PetscSFScatterBegin() 1742 1743 Collective 1744 1745 Input Arguments: 1746 + sf - star forest 1747 . unit - data type 1748 - multirootdata - root buffer to send to each leaf, one unit of data per leaf 1749 1750 Output Argument: 1751 . leafdata - leaf data to be update with personal data from each respective root 1752 1753 Level: intermediate 1754 1755 .seealso: PetscSFComputeDegreeEnd(), PetscSFScatterEnd() 1756 @*/ 1757 PetscErrorCode PetscSFScatterEnd(PetscSF sf,MPI_Datatype unit,const void *multirootdata,void *leafdata) 1758 { 1759 PetscErrorCode ierr; 1760 PetscSF multi; 1761 1762 PetscFunctionBegin; 1763 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1764 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1765 ierr = PetscSFGetMultiSF(sf,&multi);CHKERRQ(ierr); 1766 ierr = PetscSFBcastEnd(multi,unit,multirootdata,leafdata);CHKERRQ(ierr); 1767 PetscFunctionReturn(0); 1768 } 1769 1770 static PetscErrorCode PetscSFCheckLeavesUnique_Private(PetscSF sf) 1771 { 1772 #if defined(PETSC_USE_DEBUG) 1773 PetscInt i, n, nleaves; 1774 const PetscInt *ilocal = NULL; 1775 PetscHSetI seen; 1776 PetscErrorCode ierr; 1777 1778 PetscFunctionBegin; 1779 ierr = PetscSFGetGraph(sf,NULL,&nleaves,&ilocal,NULL);CHKERRQ(ierr); 1780 ierr = PetscHSetICreate(&seen);CHKERRQ(ierr); 1781 for (i = 0; i < nleaves; i++) { 1782 const PetscInt leaf = ilocal ? ilocal[i] : i; 1783 ierr = PetscHSetIAdd(seen,leaf);CHKERRQ(ierr); 1784 } 1785 ierr = PetscHSetIGetSize(seen,&n);CHKERRQ(ierr); 1786 if (n != nleaves) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Provided leaves have repeated values: all leaves must be unique"); 1787 ierr = PetscHSetIDestroy(&seen);CHKERRQ(ierr); 1788 PetscFunctionReturn(0); 1789 #else 1790 PetscFunctionBegin; 1791 PetscFunctionReturn(0); 1792 #endif 1793 } 1794 1795 /*@ 1796 PetscSFCompose - Compose a new PetscSF by putting the second SF under the first one in a top (roots) down (leaves) view 1797 1798 Input Parameters: 1799 + sfA - The first PetscSF 1800 - sfB - The second PetscSF 1801 1802 Output Parameters: 1803 . sfBA - The composite SF 1804 1805 Level: developer 1806 1807 Notes: 1808 Currently, the two SFs must be defined on congruent communicators and they must be true star 1809 forests, i.e. the same leaf is not connected with different roots. 1810 1811 sfA's leaf space and sfB's root space might be partially overlapped. The composition builds 1812 a graph with sfA's roots and sfB's leaves only when there is a path between them. Unconnected 1813 nodes (roots or leaves) are not in sfBA. Doing a Bcast on the new SF is equivalent to doing a 1814 Bcast on sfA, then a Bcast on sfB, on connected nodes. 1815 1816 .seealso: PetscSF, PetscSFComposeInverse(), PetscSFGetGraph(), PetscSFSetGraph() 1817 @*/ 1818 PetscErrorCode PetscSFCompose(PetscSF sfA,PetscSF sfB,PetscSF *sfBA) 1819 { 1820 PetscErrorCode ierr; 1821 const PetscSFNode *remotePointsA,*remotePointsB; 1822 PetscSFNode *remotePointsBA=NULL,*reorderedRemotePointsA = NULL,*leafdataB; 1823 const PetscInt *localPointsA,*localPointsB; 1824 PetscInt *localPointsBA; 1825 PetscInt i,numRootsA,numLeavesA,numRootsB,numLeavesB,minleaf,maxleaf,numLeavesBA; 1826 PetscBool denseB; 1827 1828 PetscFunctionBegin; 1829 PetscValidHeaderSpecific(sfA,PETSCSF_CLASSID,1); 1830 PetscSFCheckGraphSet(sfA,1); 1831 PetscValidHeaderSpecific(sfB,PETSCSF_CLASSID,2); 1832 PetscSFCheckGraphSet(sfB,2); 1833 PetscCheckSameComm(sfA,1,sfB,2); 1834 PetscValidPointer(sfBA,3); 1835 ierr = PetscSFCheckLeavesUnique_Private(sfA);CHKERRQ(ierr); 1836 ierr = PetscSFCheckLeavesUnique_Private(sfB);CHKERRQ(ierr); 1837 1838 ierr = PetscSFGetGraph(sfA,&numRootsA,&numLeavesA,&localPointsA,&remotePointsA);CHKERRQ(ierr); 1839 ierr = PetscSFGetGraph(sfB,&numRootsB,&numLeavesB,&localPointsB,&remotePointsB);CHKERRQ(ierr); 1840 if (localPointsA) { 1841 ierr = PetscMalloc1(numRootsB,&reorderedRemotePointsA);CHKERRQ(ierr); 1842 for (i=0; i<numRootsB; i++) { 1843 reorderedRemotePointsA[i].rank = -1; 1844 reorderedRemotePointsA[i].index = -1; 1845 } 1846 for (i=0; i<numLeavesA; i++) { 1847 if (localPointsA[i] >= numRootsB) continue; 1848 reorderedRemotePointsA[localPointsA[i]] = remotePointsA[i]; 1849 } 1850 remotePointsA = reorderedRemotePointsA; 1851 } 1852 ierr = PetscSFGetLeafRange(sfB,&minleaf,&maxleaf);CHKERRQ(ierr); 1853 ierr = PetscMalloc1(maxleaf-minleaf+1,&leafdataB);CHKERRQ(ierr); 1854 ierr = PetscSFBcastBegin(sfB,MPIU_2INT,remotePointsA,leafdataB-minleaf);CHKERRQ(ierr); 1855 ierr = PetscSFBcastEnd(sfB,MPIU_2INT,remotePointsA,leafdataB-minleaf);CHKERRQ(ierr); 1856 ierr = PetscFree(reorderedRemotePointsA);CHKERRQ(ierr); 1857 1858 denseB = (PetscBool)!localPointsB; 1859 for (i=0,numLeavesBA=0; i<numLeavesB; i++) { 1860 if (leafdataB[localPointsB ? localPointsB[i]-minleaf : i].rank == -1) denseB = PETSC_FALSE; 1861 else numLeavesBA++; 1862 } 1863 if (denseB) { 1864 localPointsBA = NULL; 1865 remotePointsBA = leafdataB; 1866 } else { 1867 ierr = PetscMalloc1(numLeavesBA,&localPointsBA);CHKERRQ(ierr); 1868 ierr = PetscMalloc1(numLeavesBA,&remotePointsBA);CHKERRQ(ierr); 1869 for (i=0,numLeavesBA=0; i<numLeavesB; i++) { 1870 const PetscInt l = localPointsB ? localPointsB[i] : i; 1871 1872 if (leafdataB[l-minleaf].rank == -1) continue; 1873 remotePointsBA[numLeavesBA] = leafdataB[l-minleaf]; 1874 localPointsBA[numLeavesBA] = l; 1875 numLeavesBA++; 1876 } 1877 ierr = PetscFree(leafdataB);CHKERRQ(ierr); 1878 } 1879 ierr = PetscSFCreate(PetscObjectComm((PetscObject)sfA),sfBA);CHKERRQ(ierr); 1880 ierr = PetscSFSetGraph(*sfBA,numRootsA,numLeavesBA,localPointsBA,PETSC_OWN_POINTER,remotePointsBA,PETSC_OWN_POINTER);CHKERRQ(ierr); 1881 PetscFunctionReturn(0); 1882 } 1883 1884 /*@ 1885 PetscSFComposeInverse - Compose a new PetscSF by putting the inverse of the second SF under the first one 1886 1887 Input Parameters: 1888 + sfA - The first PetscSF 1889 - sfB - The second PetscSF 1890 1891 Output Parameters: 1892 . sfBA - The composite SF. 1893 1894 Level: developer 1895 1896 Notes: 1897 Currently, the two SFs must be defined on congruent communicators and they must be true star 1898 forests, i.e. the same leaf is not connected with different roots. Even more, all roots of the 1899 second SF must have a degree of 1, i.e., no roots have more than one leaf connected. 1900 1901 sfA's leaf space and sfB's leaf space might be partially overlapped. The composition builds 1902 a graph with sfA's roots and sfB's roots only when there is a path between them. Unconnected 1903 roots are not in sfBA. Doing a Bcast on the new SF is equivalent to doing a Bcast on sfA, then 1904 a Reduce on sfB, on connected roots. 1905 1906 .seealso: PetscSF, PetscSFCompose(), PetscSFGetGraph(), PetscSFSetGraph(), PetscSFCreateInverseSF() 1907 @*/ 1908 PetscErrorCode PetscSFComposeInverse(PetscSF sfA,PetscSF sfB,PetscSF *sfBA) 1909 { 1910 PetscErrorCode ierr; 1911 const PetscSFNode *remotePointsA,*remotePointsB; 1912 PetscSFNode *remotePointsBA; 1913 const PetscInt *localPointsA,*localPointsB; 1914 PetscSFNode *reorderedRemotePointsA = NULL; 1915 PetscInt i,numRootsA,numLeavesA,numLeavesBA,numRootsB,numLeavesB,minleaf,maxleaf,*localPointsBA; 1916 1917 PetscFunctionBegin; 1918 PetscValidHeaderSpecific(sfA,PETSCSF_CLASSID,1); 1919 PetscSFCheckGraphSet(sfA,1); 1920 PetscValidHeaderSpecific(sfB,PETSCSF_CLASSID,2); 1921 PetscSFCheckGraphSet(sfB,2); 1922 PetscCheckSameComm(sfA,1,sfB,2); 1923 PetscValidPointer(sfBA,3); 1924 ierr = PetscSFCheckLeavesUnique_Private(sfA);CHKERRQ(ierr); 1925 ierr = PetscSFCheckLeavesUnique_Private(sfB);CHKERRQ(ierr); 1926 /* TODO: Check roots of sfB have degree of 1 */ 1927 1928 ierr = PetscSFGetGraph(sfA, &numRootsA, &numLeavesA, &localPointsA, &remotePointsA);CHKERRQ(ierr); 1929 ierr = PetscSFGetGraph(sfB, &numRootsB, &numLeavesB, &localPointsB, &remotePointsB);CHKERRQ(ierr); 1930 ierr = PetscSFGetLeafRange(sfB, &minleaf, &maxleaf);CHKERRQ(ierr); 1931 ierr = PetscMalloc1(maxleaf - minleaf + 1,&reorderedRemotePointsA);CHKERRQ(ierr); 1932 for (i=0; i<maxleaf - minleaf + 1; i++) { 1933 reorderedRemotePointsA[i].rank = -1; 1934 reorderedRemotePointsA[i].index = -1; 1935 } 1936 if (localPointsA) { 1937 for (i=0; i<numLeavesA; i++) { 1938 if (localPointsA[i] > maxleaf || localPointsA[i] < minleaf) continue; 1939 reorderedRemotePointsA[localPointsA[i] - minleaf] = remotePointsA[i]; 1940 } 1941 } else { 1942 for (i=0; i<numLeavesA; i++) { 1943 if (i > maxleaf || i < minleaf) continue; 1944 reorderedRemotePointsA[i - minleaf] = remotePointsA[i]; 1945 } 1946 } 1947 1948 ierr = PetscMalloc1(numRootsB,&localPointsBA);CHKERRQ(ierr); 1949 ierr = PetscMalloc1(numRootsB,&remotePointsBA);CHKERRQ(ierr); 1950 for (i=0; i<numRootsB; i++) { 1951 remotePointsBA[i].rank = -1; 1952 remotePointsBA[i].index = -1; 1953 } 1954 1955 /* Once we implement the TODO above (check all roots of sfB have degree of 1), we can replace the MPI_MAXLOC 1956 with MPIU_REPLACE. In that case, MPI_MAXLOC and MPIU_REPLACE have the same effect. 1957 */ 1958 ierr = PetscSFReduceBegin(sfB,MPIU_2INT,reorderedRemotePointsA-minleaf,remotePointsBA,MPI_MAXLOC);CHKERRQ(ierr); 1959 ierr = PetscSFReduceEnd(sfB,MPIU_2INT,reorderedRemotePointsA-minleaf,remotePointsBA,MPI_MAXLOC);CHKERRQ(ierr); 1960 ierr = PetscFree(reorderedRemotePointsA);CHKERRQ(ierr); 1961 for (i=0,numLeavesBA=0; i<numRootsB; i++) { 1962 if (remotePointsBA[i].rank == -1) continue; 1963 remotePointsBA[numLeavesBA].rank = remotePointsBA[i].rank; 1964 remotePointsBA[numLeavesBA].index = remotePointsBA[i].index; 1965 localPointsBA[numLeavesBA] = i; 1966 numLeavesBA++; 1967 } 1968 ierr = PetscSFCreate(PetscObjectComm((PetscObject)sfA),sfBA);CHKERRQ(ierr); 1969 ierr = PetscSFSetGraph(*sfBA,numRootsA,numLeavesBA,localPointsBA,PETSC_OWN_POINTER,remotePointsBA,PETSC_OWN_POINTER);CHKERRQ(ierr); 1970 PetscFunctionReturn(0); 1971 } 1972 1973 /* 1974 PetscSFCreateLocalSF_Private - Creates a local PetscSF that only has intra-process edges of the global PetscSF 1975 1976 Input Parameters: 1977 . sf - The global PetscSF 1978 1979 Output Parameters: 1980 . out - The local PetscSF 1981 */ 1982 PetscErrorCode PetscSFCreateLocalSF_Private(PetscSF sf,PetscSF *out) 1983 { 1984 MPI_Comm comm; 1985 PetscMPIInt myrank; 1986 const PetscInt *ilocal; 1987 const PetscSFNode *iremote; 1988 PetscInt i,j,nroots,nleaves,lnleaves,*lilocal; 1989 PetscSFNode *liremote; 1990 PetscSF lsf; 1991 PetscErrorCode ierr; 1992 1993 PetscFunctionBegin; 1994 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 1995 if (sf->ops->CreateLocalSF) { 1996 ierr = (*sf->ops->CreateLocalSF)(sf,out);CHKERRQ(ierr); 1997 } else { 1998 /* Could use PetscSFCreateEmbeddedLeafSF, but since we know the comm is PETSC_COMM_SELF, we can make it fast */ 1999 ierr = PetscObjectGetComm((PetscObject)sf,&comm);CHKERRQ(ierr); 2000 ierr = MPI_Comm_rank(comm,&myrank);CHKERRQ(ierr); 2001 2002 /* Find out local edges and build a local SF */ 2003 ierr = PetscSFGetGraph(sf,&nroots,&nleaves,&ilocal,&iremote);CHKERRQ(ierr); 2004 for (i=lnleaves=0; i<nleaves; i++) {if (iremote[i].rank == (PetscInt)myrank) lnleaves++;} 2005 ierr = PetscMalloc1(lnleaves,&lilocal);CHKERRQ(ierr); 2006 ierr = PetscMalloc1(lnleaves,&liremote);CHKERRQ(ierr); 2007 2008 for (i=j=0; i<nleaves; i++) { 2009 if (iremote[i].rank == (PetscInt)myrank) { 2010 lilocal[j] = ilocal? ilocal[i] : i; /* ilocal=NULL for contiguous storage */ 2011 liremote[j].rank = 0; /* rank in PETSC_COMM_SELF */ 2012 liremote[j].index = iremote[i].index; 2013 j++; 2014 } 2015 } 2016 ierr = PetscSFCreate(PETSC_COMM_SELF,&lsf);CHKERRQ(ierr); 2017 ierr = PetscSFSetGraph(lsf,nroots,lnleaves,lilocal,PETSC_OWN_POINTER,liremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 2018 ierr = PetscSFSetUp(lsf);CHKERRQ(ierr); 2019 *out = lsf; 2020 } 2021 PetscFunctionReturn(0); 2022 } 2023 2024 /* Similar to PetscSFBcast, but only Bcast to leaves on rank 0 */ 2025 PetscErrorCode PetscSFBcastToZero_Private(PetscSF sf,MPI_Datatype unit,const void *rootdata,void *leafdata) 2026 { 2027 PetscErrorCode ierr; 2028 PetscMemType rootmtype,leafmtype; 2029 2030 PetscFunctionBegin; 2031 PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); 2032 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 2033 ierr = PetscLogEventBegin(PETSCSF_BcastAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 2034 ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); 2035 ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); 2036 if (sf->ops->BcastToZero) { 2037 ierr = (*sf->ops->BcastToZero)(sf,unit,rootmtype,rootdata,leafmtype,leafdata);CHKERRQ(ierr); 2038 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"PetscSFBcastToZero_Private is not supported on this SF type"); 2039 ierr = PetscLogEventEnd(PETSCSF_BcastAndOpBegin,sf,0,0,0);CHKERRQ(ierr); 2040 PetscFunctionReturn(0); 2041 } 2042 2043