#include /*I "petscsf.h" I*/ #include #include #if defined(PETSC_USE_DEBUG) # define PetscSFCheckGraphSet(sf,arg) do { \ if (PetscUnlikely(!(sf)->graphset)) \ SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call PetscSFSetGraph() or PetscSFSetGraphWithPattern() on argument %D \"%s\" before %s()",(arg),#sf,PETSC_FUNCTION_NAME); \ } while (0) #else # define PetscSFCheckGraphSet(sf,arg) do {} while (0) #endif const char *const PetscSFDuplicateOptions[] = {"CONFONLY","RANKS","GRAPH","PetscSFDuplicateOption","PETSCSF_DUPLICATE_",0}; /*@ PetscSFCreate - create a star forest communication context Collective Input Arguments: . comm - communicator on which the star forest will operate Output Arguments: . sf - new star forest context Options Database Keys: + -sf_type basic -Use MPI persistent Isend/Irecv for communication (Default) . -sf_type window -Use MPI-3 one-sided window for communication - -sf_type neighbor -Use MPI-3 neighborhood collectives for communication Level: intermediate Notes: When one knows the communication graph is one of the predefined graph, such as MPI_Alltoall, MPI_Allgatherv, MPI_Gatherv, one can create a PetscSF and then set its graph with PetscSFSetGraphWithPattern(). These special SFs are optimized and they have better performance than general SFs. .seealso: PetscSFSetGraph(), PetscSFSetGraphWithPattern(), PetscSFDestroy() @*/ PetscErrorCode PetscSFCreate(MPI_Comm comm,PetscSF *sf) { PetscErrorCode ierr; PetscSF b; PetscFunctionBegin; PetscValidPointer(sf,2); ierr = PetscSFInitializePackage();CHKERRQ(ierr); ierr = PetscHeaderCreate(b,PETSCSF_CLASSID,"PetscSF","Star Forest","PetscSF",comm,PetscSFDestroy,PetscSFView);CHKERRQ(ierr); b->nroots = -1; b->nleaves = -1; b->minleaf = PETSC_MAX_INT; b->maxleaf = PETSC_MIN_INT; b->nranks = -1; b->rankorder = PETSC_TRUE; b->ingroup = MPI_GROUP_NULL; b->outgroup = MPI_GROUP_NULL; b->graphset = PETSC_FALSE; *sf = b; PetscFunctionReturn(0); } /*@ PetscSFReset - Reset a star forest so that different sizes or neighbors can be used Collective Input Arguments: . sf - star forest Level: advanced .seealso: PetscSFCreate(), PetscSFSetGraph(), PetscSFDestroy() @*/ PetscErrorCode PetscSFReset(PetscSF sf) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); if (sf->ops->Reset) {ierr = (*sf->ops->Reset)(sf);CHKERRQ(ierr);} sf->nroots = -1; sf->nleaves = -1; sf->minleaf = PETSC_MAX_INT; sf->maxleaf = PETSC_MIN_INT; sf->mine = NULL; sf->remote = NULL; sf->graphset = PETSC_FALSE; ierr = PetscFree(sf->mine_alloc);CHKERRQ(ierr); ierr = PetscFree(sf->remote_alloc);CHKERRQ(ierr); sf->nranks = -1; ierr = PetscFree4(sf->ranks,sf->roffset,sf->rmine,sf->rremote);CHKERRQ(ierr); #if defined(PETSC_HAVE_CUDA) if (sf->rmine_d) {cudaError_t err = cudaFree(sf->rmine_d);CHKERRCUDA(err);sf->rmine_d=NULL;} #endif sf->degreeknown = PETSC_FALSE; ierr = PetscFree(sf->degree);CHKERRQ(ierr); if (sf->ingroup != MPI_GROUP_NULL) {ierr = MPI_Group_free(&sf->ingroup);CHKERRQ(ierr);} if (sf->outgroup != MPI_GROUP_NULL) {ierr = MPI_Group_free(&sf->outgroup);CHKERRQ(ierr);} ierr = PetscSFDestroy(&sf->multi);CHKERRQ(ierr); ierr = PetscLayoutDestroy(&sf->map);CHKERRQ(ierr); sf->setupcalled = PETSC_FALSE; PetscFunctionReturn(0); } /*@C PetscSFSetType - Set the PetscSF communication implementation Collective on PetscSF Input Parameters: + sf - the PetscSF context - type - a known method Options Database Key: . -sf_type - Sets the method; use -help for a list of available methods (for instance, window, basic, neighbor) Notes: See "include/petscsf.h" for available methods (for instance) + PETSCSFWINDOW - MPI-2/3 one-sided - PETSCSFBASIC - basic implementation using MPI-1 two-sided Level: intermediate .seealso: PetscSFType, PetscSFCreate() @*/ PetscErrorCode PetscSFSetType(PetscSF sf,PetscSFType type) { PetscErrorCode ierr,(*r)(PetscSF); PetscBool match; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); PetscValidCharPointer(type,2); ierr = PetscObjectTypeCompare((PetscObject)sf,type,&match);CHKERRQ(ierr); if (match) PetscFunctionReturn(0); ierr = PetscFunctionListFind(PetscSFList,type,&r);CHKERRQ(ierr); if (!r) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_UNKNOWN_TYPE,"Unable to find requested PetscSF type %s",type); /* Destroy the previous PetscSF implementation context */ if (sf->ops->Destroy) {ierr = (*(sf)->ops->Destroy)(sf);CHKERRQ(ierr);} ierr = PetscMemzero(sf->ops,sizeof(*sf->ops));CHKERRQ(ierr); ierr = PetscObjectChangeTypeName((PetscObject)sf,type);CHKERRQ(ierr); ierr = (*r)(sf);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C PetscSFGetType - Get the PetscSF communication implementation Not Collective Input Parameter: . sf - the PetscSF context Output Parameter: . type - the PetscSF type name Level: intermediate .seealso: PetscSFSetType(), PetscSFCreate() @*/ PetscErrorCode PetscSFGetType(PetscSF sf, PetscSFType *type) { PetscFunctionBegin; PetscValidHeaderSpecific(sf, PETSCSF_CLASSID,1); PetscValidPointer(type,2); *type = ((PetscObject)sf)->type_name; PetscFunctionReturn(0); } /*@ PetscSFDestroy - destroy star forest Collective Input Arguments: . sf - address of star forest Level: intermediate .seealso: PetscSFCreate(), PetscSFReset() @*/ PetscErrorCode PetscSFDestroy(PetscSF *sf) { PetscErrorCode ierr; PetscFunctionBegin; if (!*sf) PetscFunctionReturn(0); PetscValidHeaderSpecific((*sf),PETSCSF_CLASSID,1); if (--((PetscObject)(*sf))->refct > 0) {*sf = NULL; PetscFunctionReturn(0);} ierr = PetscSFReset(*sf);CHKERRQ(ierr); if ((*sf)->ops->Destroy) {ierr = (*(*sf)->ops->Destroy)(*sf);CHKERRQ(ierr);} ierr = PetscHeaderDestroy(sf);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode PetscSFCheckGraphValid_Private(PetscSF sf) { #if defined(PETSC_USE_DEBUG) PetscInt i, nleaves; PetscMPIInt size; const PetscInt *ilocal; const PetscSFNode *iremote; PetscErrorCode ierr; PetscFunctionBegin; if (!sf->graphset) PetscFunctionReturn(0); ierr = PetscSFGetGraph(sf,NULL,&nleaves,&ilocal,&iremote);CHKERRQ(ierr); ierr = MPI_Comm_size(PetscObjectComm((PetscObject)sf),&size);CHKERRQ(ierr); for (i = 0; i < nleaves; i++) { const PetscInt rank = iremote[i].rank; const PetscInt remote = iremote[i].index; const PetscInt leaf = ilocal ? ilocal[i] : i; 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); if (remote < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Provided index (%D) for remote %D is invalid, should be >= 0",remote,i); if (leaf < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Provided location (%D) for leaf %D is invalid, should be >= 0",leaf,i); } PetscFunctionReturn(0); #else PetscFunctionBegin; PetscFunctionReturn(0); #endif } /*@ PetscSFSetUp - set up communication structures Collective Input Arguments: . sf - star forest communication object Level: beginner .seealso: PetscSFSetFromOptions(), PetscSFSetType() @*/ PetscErrorCode PetscSFSetUp(PetscSF sf) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); PetscSFCheckGraphSet(sf,1); if (sf->setupcalled) PetscFunctionReturn(0); ierr = PetscSFCheckGraphValid_Private(sf);CHKERRQ(ierr); if (!((PetscObject)sf)->type_name) {ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr);} ierr = PetscLogEventBegin(PETSCSF_SetUp,sf,0,0,0);CHKERRQ(ierr); if (sf->ops->SetUp) {ierr = (*sf->ops->SetUp)(sf);CHKERRQ(ierr);} ierr = PetscLogEventEnd(PETSCSF_SetUp,sf,0,0,0);CHKERRQ(ierr); sf->setupcalled = PETSC_TRUE; PetscFunctionReturn(0); } /*@ PetscSFSetFromOptions - set PetscSF options using the options database Logically Collective Input Arguments: . sf - star forest Options Database Keys: + -sf_type - implementation type, see PetscSFSetType() . -sf_rank_order - sort composite points for gathers and scatters in rank order, gathers are non-deterministic otherwise - -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. Only available for SF types of basic and neighbor. Level: intermediate @*/ PetscErrorCode PetscSFSetFromOptions(PetscSF sf) { PetscSFType deft; char type[256]; PetscErrorCode ierr; PetscBool flg; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); ierr = PetscObjectOptionsBegin((PetscObject)sf);CHKERRQ(ierr); deft = ((PetscObject)sf)->type_name ? ((PetscObject)sf)->type_name : PETSCSFBASIC; ierr = PetscOptionsFList("-sf_type","PetscSF implementation type","PetscSFSetType",PetscSFList,deft,type,sizeof(type),&flg);CHKERRQ(ierr); ierr = PetscSFSetType(sf,flg ? type : deft);CHKERRQ(ierr); 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); if (sf->ops->SetFromOptions) {ierr = (*sf->ops->SetFromOptions)(PetscOptionsObject,sf);CHKERRQ(ierr);} ierr = PetscOptionsEnd();CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ PetscSFSetRankOrder - sort multi-points for gathers and scatters by rank order Logically Collective Input Arguments: + sf - star forest - flg - PETSC_TRUE to sort, PETSC_FALSE to skip sorting (lower setup cost, but non-deterministic) Level: advanced .seealso: PetscSFGatherBegin(), PetscSFScatterBegin() @*/ PetscErrorCode PetscSFSetRankOrder(PetscSF sf,PetscBool flg) { PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); PetscValidLogicalCollectiveBool(sf,flg,2); if (sf->multi) SETERRQ(PetscObjectComm((PetscObject)sf),PETSC_ERR_ARG_WRONGSTATE,"Rank ordering must be set before first call to PetscSFGatherBegin() or PetscSFScatterBegin()"); sf->rankorder = flg; PetscFunctionReturn(0); } /*@ PetscSFSetGraph - Set a parallel star forest Collective Input Arguments: + sf - star forest . nroots - number of root vertices on the current process (these are possible targets for other process to attach leaves) . nleaves - number of leaf vertices on the current process, each of these references a root on any process . ilocal - locations of leaves in leafdata buffers, pass NULL for contiguous storage (locations must be >= 0, enforced during setup in debug mode) . localmode - copy mode for ilocal . iremote - remote locations of root vertices for each leaf on the current process (locations must be >= 0, enforced during setup in debug mode) - remotemode - copy mode for iremote Level: intermediate Notes: In Fortran you must use PETSC_COPY_VALUES for localmode and remotemode Developers Note: Local indices which are the identity permutation in the range [0,nleaves) are discarded as they encode contiguous storage. In such case, if localmode is PETSC_OWN_POINTER, the memory is deallocated as it is not needed Developers Note: This object does not necessarily encode a true star forest in the graph theoretic sense, since leaf indices are not required to be unique. Some functions, however, rely on unique leaf indices (checked in debug mode). .seealso: PetscSFCreate(), PetscSFView(), PetscSFGetGraph() @*/ PetscErrorCode PetscSFSetGraph(PetscSF sf,PetscInt nroots,PetscInt nleaves,const PetscInt *ilocal,PetscCopyMode localmode,const PetscSFNode *iremote,PetscCopyMode remotemode) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); if (nleaves > 0 && ilocal) PetscValidIntPointer(ilocal,4); if (nleaves > 0) PetscValidPointer(iremote,6); if (nroots < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nroots %D, cannot be negative",nroots); if (nleaves < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nleaves %D, cannot be negative",nleaves); if (sf->nroots >= 0) { /* Reset only if graph already set */ ierr = PetscSFReset(sf);CHKERRQ(ierr); } ierr = PetscLogEventBegin(PETSCSF_SetGraph,sf,0,0,0);CHKERRQ(ierr); sf->nroots = nroots; sf->nleaves = nleaves; if (nleaves && ilocal) { PetscInt i; PetscInt minleaf = PETSC_MAX_INT; PetscInt maxleaf = PETSC_MIN_INT; int contiguous = 1; for (i=0; iminleaf = minleaf; sf->maxleaf = maxleaf; if (contiguous) { if (localmode == PETSC_OWN_POINTER) { ierr = PetscFree(ilocal);CHKERRQ(ierr); } ilocal = NULL; } } else { sf->minleaf = 0; sf->maxleaf = nleaves - 1; } if (ilocal) { switch (localmode) { case PETSC_COPY_VALUES: ierr = PetscMalloc1(nleaves,&sf->mine_alloc);CHKERRQ(ierr); ierr = PetscArraycpy(sf->mine_alloc,ilocal,nleaves);CHKERRQ(ierr); sf->mine = sf->mine_alloc; break; case PETSC_OWN_POINTER: sf->mine_alloc = (PetscInt*)ilocal; sf->mine = sf->mine_alloc; break; case PETSC_USE_POINTER: sf->mine_alloc = NULL; sf->mine = (PetscInt*)ilocal; break; default: SETERRQ(PetscObjectComm((PetscObject)sf),PETSC_ERR_ARG_OUTOFRANGE,"Unknown localmode"); } } switch (remotemode) { case PETSC_COPY_VALUES: ierr = PetscMalloc1(nleaves,&sf->remote_alloc);CHKERRQ(ierr); ierr = PetscArraycpy(sf->remote_alloc,iremote,nleaves);CHKERRQ(ierr); sf->remote = sf->remote_alloc; break; case PETSC_OWN_POINTER: sf->remote_alloc = (PetscSFNode*)iremote; sf->remote = sf->remote_alloc; break; case PETSC_USE_POINTER: sf->remote_alloc = NULL; sf->remote = (PetscSFNode*)iremote; break; default: SETERRQ(PetscObjectComm((PetscObject)sf),PETSC_ERR_ARG_OUTOFRANGE,"Unknown remotemode"); } ierr = PetscLogEventEnd(PETSCSF_SetGraph,sf,0,0,0);CHKERRQ(ierr); sf->graphset = PETSC_TRUE; PetscFunctionReturn(0); } /*@ PetscSFSetGraphWithPattern - Sets the graph of an SF with a specific pattern Collective Input Parameters: + sf - The PetscSF . map - Layout of roots over all processes (insignificant when pattern is PETSCSF_PATTERN_ALLTOALL) - pattern - One of PETSCSF_PATTERN_ALLGATHER, PETSCSF_PATTERN_GATHER, PETSCSF_PATTERN_ALLTOALL Notes: It is easier to explain PetscSFPattern using vectors. Suppose we have an MPI vector x and its layout is map. n and N are local and global sizes of x respectively. With PETSCSF_PATTERN_ALLGATHER, the routine creates a graph that if one does Bcast on it, it will copy x to sequential vectors y on all ranks. With PETSCSF_PATTERN_GATHER, the routine creates a graph that if one does Bcast on it, it will copy x to a sequential vector y on rank 0. In above cases, entries of x are roots and entries of y are leaves. With PETSCSF_PATTERN_ALLTOALL, map is insignificant. Suppose NP is size of sf's communicator. The routine creates a graph that every rank has NP leaves and NP roots. On rank i, its leaf j is connected to root i of rank j. Here 0 <=i,j argument in SF routines. In this case, roots and leaves are symmetric. Level: intermediate @*/ PetscErrorCode PetscSFSetGraphWithPattern(PetscSF sf,PetscLayout map,PetscSFPattern pattern) { MPI_Comm comm; PetscInt n,N,res[2]; PetscMPIInt rank,size; PetscSFType type; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject)sf, &comm);CHKERRQ(ierr); if (pattern < PETSCSF_PATTERN_ALLGATHER || pattern > PETSCSF_PATTERN_ALLTOALL) SETERRQ1(comm,PETSC_ERR_ARG_OUTOFRANGE,"Unsupported PetscSFPattern %D\n",pattern); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); if (pattern == PETSCSF_PATTERN_ALLTOALL) { type = PETSCSFALLTOALL; ierr = PetscLayoutCreate(comm,&sf->map);CHKERRQ(ierr); ierr = PetscLayoutSetLocalSize(sf->map,size);CHKERRQ(ierr); ierr = PetscLayoutSetSize(sf->map,((PetscInt)size)*size);CHKERRQ(ierr); ierr = PetscLayoutSetUp(sf->map);CHKERRQ(ierr); } else { ierr = PetscLayoutGetLocalSize(map,&n);CHKERRQ(ierr); ierr = PetscLayoutGetSize(map,&N);CHKERRQ(ierr); res[0] = n; res[1] = -n; /* Check if n are same over all ranks so that we can optimize it */ ierr = MPIU_Allreduce(MPI_IN_PLACE,res,2,MPIU_INT,MPI_MAX,comm);CHKERRQ(ierr); if (res[0] == -res[1]) { /* same n */ type = (pattern == PETSCSF_PATTERN_ALLGATHER) ? PETSCSFALLGATHER : PETSCSFGATHER; } else { type = (pattern == PETSCSF_PATTERN_ALLGATHER) ? PETSCSFALLGATHERV : PETSCSFGATHERV; } ierr = PetscLayoutReference(map,&sf->map);CHKERRQ(ierr); } ierr = PetscSFSetType(sf,type);CHKERRQ(ierr); sf->pattern = pattern; sf->mine = NULL; /* Contiguous */ /* Set nleaves, nroots here in case user calls PetscSFGetGraph, which is legal to call even before PetscSFSetUp is called. Also set other easy stuff. */ if (pattern == PETSCSF_PATTERN_ALLGATHER) { sf->nleaves = N; sf->nroots = n; sf->nranks = size; sf->minleaf = 0; sf->maxleaf = N - 1; } else if (pattern == PETSCSF_PATTERN_GATHER) { sf->nleaves = rank ? 0 : N; sf->nroots = n; sf->nranks = rank ? 0 : size; sf->minleaf = 0; sf->maxleaf = rank ? -1 : N - 1; } else if (pattern == PETSCSF_PATTERN_ALLTOALL) { sf->nleaves = size; sf->nroots = size; sf->nranks = size; sf->minleaf = 0; sf->maxleaf = size - 1; } sf->ndranks = 0; /* We do not need to separate out distinguished ranks for patterned graphs to improve communication performance */ sf->graphset = PETSC_TRUE; PetscFunctionReturn(0); } /*@ PetscSFCreateInverseSF - given a PetscSF in which all vertices have degree 1, creates the inverse map Collective Input Arguments: . sf - star forest to invert Output Arguments: . isf - inverse of sf Level: advanced Notes: All roots must have degree 1. The local space may be a permutation, but cannot be sparse. .seealso: PetscSFSetGraph() @*/ PetscErrorCode PetscSFCreateInverseSF(PetscSF sf,PetscSF *isf) { PetscErrorCode ierr; PetscMPIInt rank; PetscInt i,nroots,nleaves,maxlocal,count,*newilocal; const PetscInt *ilocal; PetscSFNode *roots,*leaves; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); PetscSFCheckGraphSet(sf,1); PetscValidPointer(isf,2); ierr = PetscSFGetGraph(sf,&nroots,&nleaves,&ilocal,NULL);CHKERRQ(ierr); maxlocal = sf->maxleaf+1; /* TODO: We should use PetscSFGetLeafRange() */ ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)sf),&rank);CHKERRQ(ierr); ierr = PetscMalloc2(nroots,&roots,maxlocal,&leaves);CHKERRQ(ierr); for (i=0; i= 0) count++; if (count == nroots) newilocal = NULL; else { /* Index for sparse leaves and compact "roots" array (which is to become our leaves). */ ierr = PetscMalloc1(count,&newilocal);CHKERRQ(ierr); for (i=0,count=0; i= 0) { newilocal[count] = i; roots[count].rank = roots[i].rank; roots[count].index = roots[i].index; count++; } } } ierr = PetscSFDuplicate(sf,PETSCSF_DUPLICATE_CONFONLY,isf);CHKERRQ(ierr); ierr = PetscSFSetGraph(*isf,maxlocal,count,newilocal,PETSC_OWN_POINTER,roots,PETSC_COPY_VALUES);CHKERRQ(ierr); ierr = PetscFree2(roots,leaves);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@ PetscSFDuplicate - duplicate a PetscSF, optionally preserving rank connectivity and graph Collective Input Arguments: + sf - communication object to duplicate - opt - PETSCSF_DUPLICATE_CONFONLY, PETSCSF_DUPLICATE_RANKS, or PETSCSF_DUPLICATE_GRAPH (see PetscSFDuplicateOption) Output Arguments: . newsf - new communication object Level: beginner .seealso: PetscSFCreate(), PetscSFSetType(), PetscSFSetGraph() @*/ PetscErrorCode PetscSFDuplicate(PetscSF sf,PetscSFDuplicateOption opt,PetscSF *newsf) { PetscSFType type; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); PetscValidLogicalCollectiveEnum(sf,opt,2); PetscValidPointer(newsf,3); ierr = PetscSFCreate(PetscObjectComm((PetscObject)sf),newsf);CHKERRQ(ierr); ierr = PetscSFGetType(sf,&type);CHKERRQ(ierr); if (type) {ierr = PetscSFSetType(*newsf,type);CHKERRQ(ierr);} if (opt == PETSCSF_DUPLICATE_GRAPH) { PetscSFCheckGraphSet(sf,1); if (sf->pattern == PETSCSF_PATTERN_GENERAL) { PetscInt nroots,nleaves; const PetscInt *ilocal; const PetscSFNode *iremote; ierr = PetscSFGetGraph(sf,&nroots,&nleaves,&ilocal,&iremote);CHKERRQ(ierr); ierr = PetscSFSetGraph(*newsf,nroots,nleaves,ilocal,PETSC_COPY_VALUES,iremote,PETSC_COPY_VALUES);CHKERRQ(ierr); } else { ierr = PetscSFSetGraphWithPattern(*newsf,sf->map,sf->pattern);CHKERRQ(ierr); } } if (sf->ops->Duplicate) {ierr = (*sf->ops->Duplicate)(sf,opt,*newsf);CHKERRQ(ierr);} PetscFunctionReturn(0); } /*@C PetscSFGetGraph - Get the graph specifying a parallel star forest Not Collective Input Arguments: . sf - star forest Output Arguments: + nroots - number of root vertices on the current process (these are possible targets for other process to attach leaves) . nleaves - number of leaf vertices on the current process, each of these references a root on any process . ilocal - locations of leaves in leafdata buffers - iremote - remote locations of root vertices for each leaf on the current process Notes: We are not currently requiring that the graph is set, thus returning nroots=-1 if it has not been set yet When called from Fortran, the returned iremote array is a copy and must be deallocated after use. Consequently, if you want to update the graph, you must call PetscSFSetGraph after modifying the iremote array. Level: intermediate .seealso: PetscSFCreate(), PetscSFView(), PetscSFSetGraph() @*/ PetscErrorCode PetscSFGetGraph(PetscSF sf,PetscInt *nroots,PetscInt *nleaves,const PetscInt **ilocal,const PetscSFNode **iremote) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); if (sf->ops->GetGraph) { ierr = (sf->ops->GetGraph)(sf,nroots,nleaves,ilocal,iremote);CHKERRQ(ierr); } else { if (nroots) *nroots = sf->nroots; if (nleaves) *nleaves = sf->nleaves; if (ilocal) *ilocal = sf->mine; if (iremote) *iremote = sf->remote; } PetscFunctionReturn(0); } /*@ PetscSFGetLeafRange - Get the active leaf ranges Not Collective Input Arguments: . sf - star forest Output Arguments: + minleaf - minimum active leaf on this process. Return 0 if there are no leaves. - maxleaf - maximum active leaf on this process. Return -1 if there are no leaves. Level: developer .seealso: PetscSFCreate(), PetscSFView(), PetscSFSetGraph(), PetscSFGetGraph() @*/ PetscErrorCode PetscSFGetLeafRange(PetscSF sf,PetscInt *minleaf,PetscInt *maxleaf) { PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); PetscSFCheckGraphSet(sf,1); if (minleaf) *minleaf = sf->minleaf; if (maxleaf) *maxleaf = sf->maxleaf; PetscFunctionReturn(0); } /*@C PetscSFViewFromOptions - View from Options Collective on PetscSF Input Parameters: + A - the star forest . obj - Optional object - name - command line option Level: intermediate .seealso: PetscSF, PetscSFView, PetscObjectViewFromOptions(), PetscSFCreate() @*/ PetscErrorCode PetscSFViewFromOptions(PetscSF A,PetscObject obj,const char name[]) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(A,PETSCSF_CLASSID,1); ierr = PetscObjectViewFromOptions((PetscObject)A,obj,name);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C PetscSFView - view a star forest Collective Input Arguments: + sf - star forest - viewer - viewer to display graph, for example PETSC_VIEWER_STDOUT_WORLD Level: beginner .seealso: PetscSFCreate(), PetscSFSetGraph() @*/ PetscErrorCode PetscSFView(PetscSF sf,PetscViewer viewer) { PetscErrorCode ierr; PetscBool iascii; PetscViewerFormat format; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); if (!viewer) {ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)sf),&viewer);CHKERRQ(ierr);} PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,2); PetscCheckSameComm(sf,1,viewer,2); if (sf->graphset) {ierr = PetscSFSetUp(sf);CHKERRQ(ierr);} ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); if (iascii) { PetscMPIInt rank; PetscInt ii,i,j; ierr = PetscObjectPrintClassNamePrefixType((PetscObject)sf,viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); if (sf->ops->View) {ierr = (*sf->ops->View)(sf,viewer);CHKERRQ(ierr);} if (sf->pattern == PETSCSF_PATTERN_GENERAL) { if (!sf->graphset) { ierr = PetscViewerASCIIPrintf(viewer,"PetscSFSetGraph() has not been called yet\n");CHKERRQ(ierr); ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); PetscFunctionReturn(0); } ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)sf),&rank);CHKERRQ(ierr); ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Number of roots=%D, leaves=%D, remote ranks=%D\n",rank,sf->nroots,sf->nleaves,sf->nranks);CHKERRQ(ierr); for (i=0; inleaves; i++) { 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); } ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { PetscMPIInt *tmpranks,*perm; ierr = PetscMalloc2(sf->nranks,&tmpranks,sf->nranks,&perm);CHKERRQ(ierr); ierr = PetscArraycpy(tmpranks,sf->ranks,sf->nranks);CHKERRQ(ierr); for (i=0; inranks; i++) perm[i] = i; ierr = PetscSortMPIIntWithArray(sf->nranks,tmpranks,perm);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Roots referenced by my leaves, by rank\n",rank);CHKERRQ(ierr); for (ii=0; iinranks; ii++) { i = perm[ii]; ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] %d: %D edges\n",rank,sf->ranks[i],sf->roffset[i+1]-sf->roffset[i]);CHKERRQ(ierr); for (j=sf->roffset[i]; jroffset[i+1]; j++) { ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] %D <- %D\n",rank,sf->rmine[j],sf->rremote[j]);CHKERRQ(ierr); } } ierr = PetscFree2(tmpranks,perm);CHKERRQ(ierr); } ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); } ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); } PetscFunctionReturn(0); } /*@C PetscSFGetRootRanks - Get root ranks and number of vertices referenced by leaves on this process Not Collective Input Arguments: . sf - star forest Output Arguments: + nranks - number of ranks referenced by local part . ranks - array of ranks . roffset - offset in rmine/rremote for each rank (length nranks+1) . rmine - concatenated array holding local indices referencing each remote rank - rremote - concatenated array holding remote indices referenced for each remote rank Level: developer .seealso: PetscSFGetLeafRanks() @*/ PetscErrorCode PetscSFGetRootRanks(PetscSF sf,PetscInt *nranks,const PetscMPIInt **ranks,const PetscInt **roffset,const PetscInt **rmine,const PetscInt **rremote) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); if (!sf->setupcalled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call PetscSFSetUp() before obtaining ranks"); if (sf->ops->GetRootRanks) { ierr = (sf->ops->GetRootRanks)(sf,nranks,ranks,roffset,rmine,rremote);CHKERRQ(ierr); } else { /* The generic implementation */ if (nranks) *nranks = sf->nranks; if (ranks) *ranks = sf->ranks; if (roffset) *roffset = sf->roffset; if (rmine) *rmine = sf->rmine; if (rremote) *rremote = sf->rremote; } PetscFunctionReturn(0); } /*@C PetscSFGetLeafRanks - Get leaf ranks referencing roots on this process Not Collective Input Arguments: . sf - star forest Output Arguments: + niranks - number of leaf ranks referencing roots on this process . iranks - array of ranks . ioffset - offset in irootloc for each rank (length niranks+1) - irootloc - concatenated array holding local indices of roots referenced by each leaf rank Level: developer .seealso: PetscSFGetRootRanks() @*/ PetscErrorCode PetscSFGetLeafRanks(PetscSF sf,PetscInt *niranks,const PetscMPIInt **iranks,const PetscInt **ioffset,const PetscInt **irootloc) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); if (!sf->setupcalled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call PetscSFSetUp() before obtaining ranks"); if (sf->ops->GetLeafRanks) { ierr = (sf->ops->GetLeafRanks)(sf,niranks,iranks,ioffset,irootloc);CHKERRQ(ierr); } else { PetscSFType type; ierr = PetscSFGetType(sf,&type);CHKERRQ(ierr); SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"PetscSFGetLeafRanks() is not supported on this StarForest type: %s", type); } PetscFunctionReturn(0); } static PetscBool InList(PetscMPIInt needle,PetscMPIInt n,const PetscMPIInt *list) { PetscInt i; for (i=0; inleaves; i++) { /* Log 1-based rank */ ierr = PetscTableAdd(table,sf->remote[i].rank+1,1,ADD_VALUES);CHKERRQ(ierr); } ierr = PetscTableGetCount(table,&sf->nranks);CHKERRQ(ierr); ierr = PetscMalloc4(sf->nranks,&sf->ranks,sf->nranks+1,&sf->roffset,sf->nleaves,&sf->rmine,sf->nleaves,&sf->rremote);CHKERRQ(ierr); ierr = PetscMalloc2(sf->nranks,&rcount,sf->nranks,&ranks);CHKERRQ(ierr); ierr = PetscTableGetHeadPosition(table,&pos);CHKERRQ(ierr); for (i=0; inranks; i++) { ierr = PetscTableGetNext(table,&pos,&ranks[i],&rcount[i]);CHKERRQ(ierr); ranks[i]--; /* Convert back to 0-based */ } ierr = PetscTableDestroy(&table);CHKERRQ(ierr); /* We expect that dgroup is reliably "small" while nranks could be large */ { MPI_Group group = MPI_GROUP_NULL; PetscMPIInt *dgroupranks; ierr = MPI_Comm_group(PetscObjectComm((PetscObject)sf),&group);CHKERRQ(ierr); ierr = MPI_Group_size(dgroup,&groupsize);CHKERRQ(ierr); ierr = PetscMalloc1(groupsize,&dgroupranks);CHKERRQ(ierr); ierr = PetscMalloc1(groupsize,&groupranks);CHKERRQ(ierr); for (i=0; indranks) followed by non-distinguished */ for (sf->ndranks=0,i=sf->nranks; sf->ndranksndranksndranks<=i; sf->ndranks++) { /* Scan sf->ndranks forward looking for non-distinguished rank */ if (!InList(ranks[sf->ndranks],groupsize,groupranks)) break; } if (sf->ndranks < i) { /* Swap ranks[sf->ndranks] with ranks[i] */ PetscInt tmprank,tmpcount; tmprank = ranks[i]; tmpcount = rcount[i]; ranks[i] = ranks[sf->ndranks]; rcount[i] = rcount[sf->ndranks]; ranks[sf->ndranks] = tmprank; rcount[sf->ndranks] = tmpcount; sf->ndranks++; } } ierr = PetscFree(groupranks);CHKERRQ(ierr); ierr = PetscSortIntWithArray(sf->ndranks,ranks,rcount);CHKERRQ(ierr); ierr = PetscSortIntWithArray(sf->nranks-sf->ndranks,ranks+sf->ndranks,rcount+sf->ndranks);CHKERRQ(ierr); sf->roffset[0] = 0; for (i=0; inranks; i++) { ierr = PetscMPIIntCast(ranks[i],sf->ranks+i);CHKERRQ(ierr); sf->roffset[i+1] = sf->roffset[i] + rcount[i]; rcount[i] = 0; } for (i=0, irank = -1, orank = -1; inleaves; i++) { /* short circuit */ if (orank != sf->remote[i].rank) { /* Search for index of iremote[i].rank in sf->ranks */ ierr = PetscFindMPIInt(sf->remote[i].rank,sf->ndranks,sf->ranks,&irank);CHKERRQ(ierr); if (irank < 0) { ierr = PetscFindMPIInt(sf->remote[i].rank,sf->nranks-sf->ndranks,sf->ranks+sf->ndranks,&irank);CHKERRQ(ierr); if (irank >= 0) irank += sf->ndranks; } orank = sf->remote[i].rank; } if (irank < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Could not find rank %D in array",sf->remote[i].rank); sf->rmine[sf->roffset[irank] + rcount[irank]] = sf->mine ? sf->mine[i] : i; sf->rremote[sf->roffset[irank] + rcount[irank]] = sf->remote[i].index; rcount[irank]++; } ierr = PetscFree2(rcount,ranks);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C PetscSFGetGroups - gets incoming and outgoing process groups Collective Input Argument: . sf - star forest Output Arguments: + incoming - group of origin processes for incoming edges (leaves that reference my roots) - outgoing - group of destination processes for outgoing edges (roots that I reference) Level: developer .seealso: PetscSFGetWindow(), PetscSFRestoreWindow() @*/ PetscErrorCode PetscSFGetGroups(PetscSF sf,MPI_Group *incoming,MPI_Group *outgoing) { PetscErrorCode ierr; MPI_Group group = MPI_GROUP_NULL; PetscFunctionBegin; if (sf->nranks < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call PetscSFSetUpRanks() before obtaining groups"); if (sf->ingroup == MPI_GROUP_NULL) { PetscInt i; const PetscInt *indegree; PetscMPIInt rank,*outranks,*inranks; PetscSFNode *remote; PetscSF bgcount; /* Compute the number of incoming ranks */ ierr = PetscMalloc1(sf->nranks,&remote);CHKERRQ(ierr); for (i=0; inranks; i++) { remote[i].rank = sf->ranks[i]; remote[i].index = 0; } ierr = PetscSFDuplicate(sf,PETSCSF_DUPLICATE_CONFONLY,&bgcount);CHKERRQ(ierr); ierr = PetscSFSetGraph(bgcount,1,sf->nranks,NULL,PETSC_COPY_VALUES,remote,PETSC_OWN_POINTER);CHKERRQ(ierr); ierr = PetscSFComputeDegreeBegin(bgcount,&indegree);CHKERRQ(ierr); ierr = PetscSFComputeDegreeEnd(bgcount,&indegree);CHKERRQ(ierr); /* Enumerate the incoming ranks */ ierr = PetscMalloc2(indegree[0],&inranks,sf->nranks,&outranks);CHKERRQ(ierr); ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)sf),&rank);CHKERRQ(ierr); for (i=0; inranks; i++) outranks[i] = rank; ierr = PetscSFGatherBegin(bgcount,MPI_INT,outranks,inranks);CHKERRQ(ierr); ierr = PetscSFGatherEnd(bgcount,MPI_INT,outranks,inranks);CHKERRQ(ierr); ierr = MPI_Comm_group(PetscObjectComm((PetscObject)sf),&group);CHKERRQ(ierr); ierr = MPI_Group_incl(group,indegree[0],inranks,&sf->ingroup);CHKERRQ(ierr); ierr = MPI_Group_free(&group);CHKERRQ(ierr); ierr = PetscFree2(inranks,outranks);CHKERRQ(ierr); ierr = PetscSFDestroy(&bgcount);CHKERRQ(ierr); } *incoming = sf->ingroup; if (sf->outgroup == MPI_GROUP_NULL) { ierr = MPI_Comm_group(PetscObjectComm((PetscObject)sf),&group);CHKERRQ(ierr); ierr = MPI_Group_incl(group,sf->nranks,sf->ranks,&sf->outgroup);CHKERRQ(ierr); ierr = MPI_Group_free(&group);CHKERRQ(ierr); } *outgoing = sf->outgroup; PetscFunctionReturn(0); } /*@ PetscSFGetMultiSF - gets the inner SF implemeting gathers and scatters Collective Input Argument: . sf - star forest that may contain roots with 0 or with more than 1 vertex Output Arguments: . multi - star forest with split roots, such that each root has degree exactly 1 Level: developer Notes: In most cases, users should use PetscSFGatherBegin() and PetscSFScatterBegin() instead of manipulating multi directly. Since multi satisfies the stronger condition that each entry in the global space has exactly one incoming edge, it is a candidate for future optimization that might involve its removal. .seealso: PetscSFSetGraph(), PetscSFGatherBegin(), PetscSFScatterBegin(), PetscSFComputeMultiRootOriginalNumbering() @*/ PetscErrorCode PetscSFGetMultiSF(PetscSF sf,PetscSF *multi) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); PetscValidPointer(multi,2); if (sf->nroots < 0) { /* Graph has not been set yet; why do we need this? */ ierr = PetscSFDuplicate(sf,PETSCSF_DUPLICATE_RANKS,&sf->multi);CHKERRQ(ierr); *multi = sf->multi; PetscFunctionReturn(0); } if (!sf->multi) { const PetscInt *indegree; PetscInt i,*inoffset,*outones,*outoffset,maxlocal; PetscSFNode *remote; maxlocal = sf->maxleaf+1; /* TODO: We should use PetscSFGetLeafRange() */ ierr = PetscSFComputeDegreeBegin(sf,&indegree);CHKERRQ(ierr); ierr = PetscSFComputeDegreeEnd(sf,&indegree);CHKERRQ(ierr); ierr = PetscMalloc3(sf->nroots+1,&inoffset,maxlocal,&outones,maxlocal,&outoffset);CHKERRQ(ierr); inoffset[0] = 0; for (i=0; inroots; i++) inoffset[i+1] = inoffset[i] + indegree[i]; for (i=0; inroots; i++) inoffset[i] -= indegree[i]; /* Undo the increment */ #if defined(PETSC_USE_DEBUG) /* Check that the expected number of increments occurred */ for (i=0; inroots; i++) { if (inoffset[i] + indegree[i] != inoffset[i+1]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect result after PetscSFFetchAndOp"); } #endif ierr = PetscMalloc1(sf->nleaves,&remote);CHKERRQ(ierr); for (i=0; inleaves; i++) { remote[i].rank = sf->remote[i].rank; remote[i].index = outoffset[sf->mine ? sf->mine[i] : i]; } ierr = PetscSFDuplicate(sf,PETSCSF_DUPLICATE_RANKS,&sf->multi);CHKERRQ(ierr); ierr = PetscSFSetGraph(sf->multi,inoffset[sf->nroots],sf->nleaves,sf->mine,PETSC_COPY_VALUES,remote,PETSC_OWN_POINTER);CHKERRQ(ierr); if (sf->rankorder) { /* Sort the ranks */ PetscMPIInt rank; PetscInt *inranks,*newoffset,*outranks,*newoutoffset,*tmpoffset,maxdegree; PetscSFNode *newremote; ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)sf),&rank);CHKERRQ(ierr); for (i=0,maxdegree=0; inroots; i++) maxdegree = PetscMax(maxdegree,indegree[i]); ierr = PetscMalloc5(sf->multi->nroots,&inranks,sf->multi->nroots,&newoffset,maxlocal,&outranks,maxlocal,&newoutoffset,maxdegree,&tmpoffset);CHKERRQ(ierr); for (i=0; imulti,MPIU_INT,outranks,inranks,MPIU_REPLACE);CHKERRQ(ierr); ierr = PetscSFReduceEnd(sf->multi,MPIU_INT,outranks,inranks,MPIU_REPLACE);CHKERRQ(ierr); /* Sort the incoming ranks at each vertex, build the inverse map */ for (i=0; inroots; i++) { PetscInt j; for (j=0; jmulti,MPIU_INT,newoffset,newoutoffset);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sf->multi,MPIU_INT,newoffset,newoutoffset);CHKERRQ(ierr); ierr = PetscMalloc1(sf->nleaves,&newremote);CHKERRQ(ierr); for (i=0; inleaves; i++) { newremote[i].rank = sf->remote[i].rank; newremote[i].index = newoutoffset[sf->mine ? sf->mine[i] : i]; } ierr = PetscSFSetGraph(sf->multi,inoffset[sf->nroots],sf->nleaves,sf->mine,PETSC_COPY_VALUES,newremote,PETSC_OWN_POINTER);CHKERRQ(ierr); ierr = PetscFree5(inranks,newoffset,outranks,newoutoffset,tmpoffset);CHKERRQ(ierr); } ierr = PetscFree3(inoffset,outones,outoffset);CHKERRQ(ierr); } *multi = sf->multi; PetscFunctionReturn(0); } /*@C PetscSFCreateEmbeddedSF - removes edges from all but the selected roots, does not remap indices Collective Input Arguments: + sf - original star forest . nselected - number of selected roots on this process - selected - indices of the selected roots on this process Output Arguments: . newsf - new star forest Level: advanced Note: To use the new PetscSF, it may be necessary to know the indices of the leaves that are still participating. This can be done by calling PetscSFGetGraph(). .seealso: PetscSFSetGraph(), PetscSFGetGraph() @*/ PetscErrorCode PetscSFCreateEmbeddedSF(PetscSF sf,PetscInt nselected,const PetscInt *selected,PetscSF *newsf) { PetscInt i,n,*roots,*rootdata,*leafdata,nroots,nleaves,connected_leaves,*new_ilocal; const PetscSFNode *iremote; PetscSFNode *new_iremote; PetscSF tmpsf; MPI_Comm comm; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); PetscSFCheckGraphSet(sf,1); if (nselected) PetscValidPointer(selected,3); PetscValidPointer(newsf,4); ierr = PetscSFSetUp(sf);CHKERRQ(ierr); ierr = PetscLogEventBegin(PETSCSF_EmbedSF,sf,0,0,0);CHKERRQ(ierr); /* Uniq selected[] and put results in roots[] */ ierr = PetscObjectGetComm((PetscObject)sf,&comm);CHKERRQ(ierr); ierr = PetscMalloc1(nselected,&roots);CHKERRQ(ierr); ierr = PetscArraycpy(roots,selected,nselected);CHKERRQ(ierr); ierr = PetscSortedRemoveDupsInt(&nselected,roots);CHKERRQ(ierr); 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); if (sf->ops->CreateEmbeddedSF) { ierr = (*sf->ops->CreateEmbeddedSF)(sf,nselected,roots,newsf);CHKERRQ(ierr); } else { /* A generic version of creating embedded sf. Note that we called PetscSFSetGraph() twice, which is certainly expensive */ /* Find out which leaves (not leaf data items) are still connected to roots in the embedded sf */ ierr = PetscSFGetGraph(sf,&nroots,&nleaves,NULL,&iremote);CHKERRQ(ierr); ierr = PetscSFDuplicate(sf,PETSCSF_DUPLICATE_RANKS,&tmpsf);CHKERRQ(ierr); ierr = PetscSFSetGraph(tmpsf,nroots,nleaves,NULL/*contiguous*/,PETSC_USE_POINTER,iremote,PETSC_USE_POINTER);CHKERRQ(ierr); ierr = PetscCalloc2(nroots,&rootdata,nleaves,&leafdata);CHKERRQ(ierr); for (i=0; imine ? sf->mine[i] : i; new_iremote[n].rank = sf->remote[i].rank; new_iremote[n].index = sf->remote[i].index; ++n; } } 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); ierr = PetscSFDuplicate(sf,PETSCSF_DUPLICATE_CONFONLY,newsf);CHKERRQ(ierr); ierr = PetscSFSetGraph(*newsf,nroots,connected_leaves,new_ilocal,PETSC_OWN_POINTER,new_iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); ierr = PetscFree2(rootdata,leafdata);CHKERRQ(ierr); } ierr = PetscFree(roots);CHKERRQ(ierr); ierr = PetscSFSetUp(*newsf);CHKERRQ(ierr); ierr = PetscLogEventEnd(PETSCSF_EmbedSF,sf,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C PetscSFCreateEmbeddedLeafSF - removes edges from all but the selected leaves, does not remap indices Collective Input Arguments: + sf - original star forest . nselected - number of selected leaves on this process - selected - indices of the selected leaves on this process Output Arguments: . newsf - new star forest Level: advanced .seealso: PetscSFCreateEmbeddedSF(), PetscSFSetGraph(), PetscSFGetGraph() @*/ PetscErrorCode PetscSFCreateEmbeddedLeafSF(PetscSF sf,PetscInt nselected,const PetscInt *selected,PetscSF *newsf) { const PetscSFNode *iremote; PetscSFNode *new_iremote; const PetscInt *ilocal; PetscInt i,nroots,*leaves,*new_ilocal; MPI_Comm comm; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); PetscSFCheckGraphSet(sf,1); if (nselected) PetscValidPointer(selected,3); PetscValidPointer(newsf,4); /* Uniq selected[] and put results in leaves[] */ ierr = PetscObjectGetComm((PetscObject)sf,&comm);CHKERRQ(ierr); ierr = PetscMalloc1(nselected,&leaves);CHKERRQ(ierr); ierr = PetscArraycpy(leaves,selected,nselected);CHKERRQ(ierr); ierr = PetscSortedRemoveDupsInt(&nselected,leaves);CHKERRQ(ierr); 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); /* Optimize the routine only when sf is setup and hence we can reuse sf's communication pattern */ if (sf->setupcalled && sf->ops->CreateEmbeddedLeafSF) { ierr = (*sf->ops->CreateEmbeddedLeafSF)(sf,nselected,leaves,newsf);CHKERRQ(ierr); } else { ierr = PetscSFGetGraph(sf,&nroots,NULL,&ilocal,&iremote);CHKERRQ(ierr); ierr = PetscMalloc1(nselected,&new_ilocal);CHKERRQ(ierr); ierr = PetscMalloc1(nselected,&new_iremote);CHKERRQ(ierr); for (i=0; iops->BcastAndOpBegin)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,op);CHKERRQ(ierr); ierr = PetscLogEventEnd(PETSCSF_BcastAndOpBegin,sf,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C PetscSFBcastAndOpEnd - end a broadcast & reduce operation started with PetscSFBcastAndOpBegin() Collective Input Arguments: + sf - star forest . unit - data type . rootdata - buffer to broadcast - op - operation to use for reduction Output Arguments: . leafdata - buffer to be reduced with values from each leaf's respective root Level: intermediate .seealso: PetscSFSetGraph(), PetscSFReduceEnd() @*/ PetscErrorCode PetscSFBcastAndOpEnd(PetscSF sf,MPI_Datatype unit,const void *rootdata,void *leafdata,MPI_Op op) { PetscErrorCode ierr; PetscMemType rootmtype,leafmtype; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); ierr = PetscSFSetUp(sf);CHKERRQ(ierr); ierr = PetscLogEventBegin(PETSCSF_BcastAndOpEnd,sf,0,0,0);CHKERRQ(ierr); ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); ierr = (*sf->ops->BcastAndOpEnd)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,op);CHKERRQ(ierr); ierr = PetscLogEventEnd(PETSCSF_BcastAndOpEnd,sf,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C PetscSFReduceBegin - begin reduction of leafdata into rootdata, to be completed with call to PetscSFReduceEnd() Collective Input Arguments: + sf - star forest . unit - data type . leafdata - values to reduce - op - reduction operation Output Arguments: . rootdata - result of reduction of values from all leaves of each root Level: intermediate .seealso: PetscSFBcastBegin() @*/ PetscErrorCode PetscSFReduceBegin(PetscSF sf,MPI_Datatype unit,const void *leafdata,void *rootdata,MPI_Op op) { PetscErrorCode ierr; PetscMemType rootmtype,leafmtype; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); ierr = PetscSFSetUp(sf);CHKERRQ(ierr); ierr = PetscLogEventBegin(PETSCSF_ReduceBegin,sf,0,0,0);CHKERRQ(ierr); ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); #if defined(PETSC_HAVE_CUDA) if (rootmtype == PETSC_MEMTYPE_DEVICE || leafmtype == PETSC_MEMTYPE_DEVICE) {cudaError_t err = cudaDeviceSynchronize();CHKERRCUDA(err);} #endif ierr = (sf->ops->ReduceBegin)(sf,unit,leafmtype,leafdata,rootmtype,rootdata,op);CHKERRQ(ierr); ierr = PetscLogEventEnd(PETSCSF_ReduceBegin,sf,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C PetscSFReduceEnd - end a reduction operation started with PetscSFReduceBegin() Collective Input Arguments: + sf - star forest . unit - data type . leafdata - values to reduce - op - reduction operation Output Arguments: . rootdata - result of reduction of values from all leaves of each root Level: intermediate .seealso: PetscSFSetGraph(), PetscSFBcastEnd() @*/ PetscErrorCode PetscSFReduceEnd(PetscSF sf,MPI_Datatype unit,const void *leafdata,void *rootdata,MPI_Op op) { PetscErrorCode ierr; PetscMemType rootmtype,leafmtype; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); ierr = PetscSFSetUp(sf);CHKERRQ(ierr); ierr = PetscLogEventBegin(PETSCSF_ReduceEnd,sf,0,0,0);CHKERRQ(ierr); ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); ierr = (*sf->ops->ReduceEnd)(sf,unit,leafmtype,leafdata,rootmtype,rootdata,op);CHKERRQ(ierr); ierr = PetscLogEventEnd(PETSCSF_ReduceEnd,sf,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C PetscSFFetchAndOpBegin - begin operation that fetches values from root and updates atomically by applying operation using my leaf value, to be completed with PetscSFFetchAndOpEnd() Collective Input Arguments: + sf - star forest . unit - data type . leafdata - leaf values to use in reduction - op - operation to use for reduction Output Arguments: + rootdata - root values to be updated, input state is seen by first process to perform an update - leafupdate - state at each leaf's respective root immediately prior to my atomic update Level: advanced Note: The update is only atomic at the granularity provided by the hardware. Different roots referenced by the same process might be updated in a different order. Furthermore, if a composite type is used for the unit datatype, atomicity is not guaranteed across the whole vertex. Therefore, this function is mostly only used with primitive types such as integers. .seealso: PetscSFComputeDegreeBegin(), PetscSFReduceBegin(), PetscSFSetGraph() @*/ PetscErrorCode PetscSFFetchAndOpBegin(PetscSF sf,MPI_Datatype unit,void *rootdata,const void *leafdata,void *leafupdate,MPI_Op op) { PetscErrorCode ierr; PetscMemType rootmtype,leafmtype,leafupdatemtype; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); ierr = PetscSFSetUp(sf);CHKERRQ(ierr); ierr = PetscLogEventBegin(PETSCSF_FetchAndOpBegin,sf,0,0,0);CHKERRQ(ierr); ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); ierr = PetscGetMemType(leafupdate,&leafupdatemtype);CHKERRQ(ierr); if (leafmtype != leafupdatemtype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for leafdata and leafupdate in different memory types"); #if defined(PETSC_HAVE_CUDA) if (rootmtype == PETSC_MEMTYPE_DEVICE || leafmtype == PETSC_MEMTYPE_DEVICE) {cudaError_t err = cudaDeviceSynchronize();CHKERRCUDA(err);} #endif ierr = (*sf->ops->FetchAndOpBegin)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,leafupdate,op);CHKERRQ(ierr); ierr = PetscLogEventEnd(PETSCSF_FetchAndOpBegin,sf,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C PetscSFFetchAndOpEnd - end operation started in matching call to PetscSFFetchAndOpBegin() to fetch values from roots and update atomically by applying operation using my leaf value Collective Input Arguments: + sf - star forest . unit - data type . leafdata - leaf values to use in reduction - op - operation to use for reduction Output Arguments: + rootdata - root values to be updated, input state is seen by first process to perform an update - leafupdate - state at each leaf's respective root immediately prior to my atomic update Level: advanced .seealso: PetscSFComputeDegreeEnd(), PetscSFReduceEnd(), PetscSFSetGraph() @*/ PetscErrorCode PetscSFFetchAndOpEnd(PetscSF sf,MPI_Datatype unit,void *rootdata,const void *leafdata,void *leafupdate,MPI_Op op) { PetscErrorCode ierr; PetscMemType rootmtype,leafmtype,leafupdatemtype; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); ierr = PetscSFSetUp(sf);CHKERRQ(ierr); ierr = PetscLogEventBegin(PETSCSF_FetchAndOpEnd,sf,0,0,0);CHKERRQ(ierr); ierr = PetscGetMemType(rootdata,&rootmtype);CHKERRQ(ierr); ierr = PetscGetMemType(leafdata,&leafmtype);CHKERRQ(ierr); ierr = PetscGetMemType(leafupdate,&leafupdatemtype);CHKERRQ(ierr); if (leafmtype != leafupdatemtype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for leafdata and leafupdate in different memory types"); ierr = (*sf->ops->FetchAndOpEnd)(sf,unit,rootmtype,rootdata,leafmtype,leafdata,leafupdate,op);CHKERRQ(ierr); ierr = PetscLogEventEnd(PETSCSF_FetchAndOpEnd,sf,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /*@C PetscSFComputeDegreeBegin - begin computation of degree for each root vertex, to be completed with PetscSFComputeDegreeEnd() Collective Input Arguments: . sf - star forest Output Arguments: . degree - degree of each root vertex Level: advanced Notes: The returned array is owned by PetscSF and automatically freed by PetscSFDestroy(). Hence no need to call PetscFree() on it. .seealso: PetscSFGatherBegin() @*/ PetscErrorCode PetscSFComputeDegreeBegin(PetscSF sf,const PetscInt **degree) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); PetscSFCheckGraphSet(sf,1); PetscValidPointer(degree,2); if (!sf->degreeknown) { PetscInt i, nroots = sf->nroots, maxlocal; if (sf->degree) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Calls to PetscSFComputeDegreeBegin() cannot be nested."); maxlocal = sf->maxleaf-sf->minleaf+1; ierr = PetscMalloc1(nroots,&sf->degree);CHKERRQ(ierr); ierr = PetscMalloc1(PetscMax(maxlocal,1),&sf->degreetmp);CHKERRQ(ierr); /* allocate at least one entry, see check in PetscSFComputeDegreeEnd() */ for (i=0; idegree[i] = 0; for (i=0; idegreetmp[i] = 1; ierr = PetscSFReduceBegin(sf,MPIU_INT,sf->degreetmp-sf->minleaf,sf->degree,MPI_SUM);CHKERRQ(ierr); } *degree = NULL; PetscFunctionReturn(0); } /*@C PetscSFComputeDegreeEnd - complete computation of degree for each root vertex, started with PetscSFComputeDegreeBegin() Collective Input Arguments: . sf - star forest Output Arguments: . degree - degree of each root vertex Level: developer Notes: The returned array is owned by PetscSF and automatically freed by PetscSFDestroy(). Hence no need to call PetscFree() on it. .seealso: @*/ PetscErrorCode PetscSFComputeDegreeEnd(PetscSF sf,const PetscInt **degree) { PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); PetscSFCheckGraphSet(sf,1); PetscValidPointer(degree,2); if (!sf->degreeknown) { if (!sf->degreetmp) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Must call PetscSFComputeDegreeBegin() before PetscSFComputeDegreeEnd()"); ierr = PetscSFReduceEnd(sf,MPIU_INT,sf->degreetmp-sf->minleaf,sf->degree,MPI_SUM);CHKERRQ(ierr); ierr = PetscFree(sf->degreetmp);CHKERRQ(ierr); sf->degreeknown = PETSC_TRUE; } *degree = sf->degree; PetscFunctionReturn(0); } /*@C PetscSFComputeMultiRootOriginalNumbering - Returns original numbering of multi-roots (roots of multi-SF returned by PetscSFGetMultiSF()). Each multi-root is assigned index of the corresponding original root. Collective Input Arguments: + sf - star forest - degree - degree of each root vertex, computed with PetscSFComputeDegreeBegin()/PetscSFComputeDegreeEnd() Output Arguments: + nMultiRoots - (optional) number of multi-roots (roots of multi-SF) - multiRootsOrigNumbering - original indices of multi-roots; length of this array is nMultiRoots Level: developer Notes: The returned array multiRootsOrigNumbering is newly allocated and should be destroyed with PetscFree() when no longer needed. .seealso: PetscSFComputeDegreeBegin(), PetscSFComputeDegreeEnd(), PetscSFGetMultiSF() @*/ PetscErrorCode PetscSFComputeMultiRootOriginalNumbering(PetscSF sf, const PetscInt degree[], PetscInt *nMultiRoots, PetscInt *multiRootsOrigNumbering[]) { PetscSF msf; PetscInt i, j, k, nroots, nmroots; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(sf,PETSCSF_CLASSID,1); ierr = PetscSFGetGraph(sf, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); if (nroots) PetscValidIntPointer(degree,2); if (nMultiRoots) PetscValidIntPointer(nMultiRoots,3); PetscValidPointer(multiRootsOrigNumbering,4); ierr = PetscSFGetMultiSF(sf,&msf);CHKERRQ(ierr); ierr = PetscSFGetGraph(msf, &nmroots, NULL, NULL, NULL);CHKERRQ(ierr); ierr = PetscMalloc1(nmroots, multiRootsOrigNumbering);CHKERRQ(ierr); for (i=0,j=0,k=0; i= numRootsB) continue; reorderedRemotePointsA[localPointsA[i]] = remotePointsA[i]; } remotePointsA = reorderedRemotePointsA; } ierr = PetscSFGetLeafRange(sfB,&minleaf,&maxleaf);CHKERRQ(ierr); ierr = PetscMalloc1(maxleaf-minleaf+1,&leafdataB);CHKERRQ(ierr); ierr = PetscSFBcastBegin(sfB,MPIU_2INT,remotePointsA,leafdataB-minleaf);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sfB,MPIU_2INT,remotePointsA,leafdataB-minleaf);CHKERRQ(ierr); ierr = PetscFree(reorderedRemotePointsA);CHKERRQ(ierr); denseB = (PetscBool)!localPointsB; for (i=0,numLeavesBA=0; i maxleaf || localPointsA[i] < minleaf) continue; reorderedRemotePointsA[localPointsA[i] - minleaf] = remotePointsA[i]; } } else { for (i=0; i maxleaf || i < minleaf) continue; reorderedRemotePointsA[i - minleaf] = remotePointsA[i]; } } ierr = PetscMalloc1(numRootsB,&localPointsBA);CHKERRQ(ierr); ierr = PetscMalloc1(numRootsB,&remotePointsBA);CHKERRQ(ierr); for (i=0; iops->CreateLocalSF) { ierr = (*sf->ops->CreateLocalSF)(sf,out);CHKERRQ(ierr); } else { /* Could use PetscSFCreateEmbeddedLeafSF, but since we know the comm is PETSC_COMM_SELF, we can make it fast */ ierr = PetscObjectGetComm((PetscObject)sf,&comm);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&myrank);CHKERRQ(ierr); /* Find out local edges and build a local SF */ ierr = PetscSFGetGraph(sf,&nroots,&nleaves,&ilocal,&iremote);CHKERRQ(ierr); for (i=lnleaves=0; iops->BcastToZero) { ierr = (*sf->ops->BcastToZero)(sf,unit,rootmtype,rootdata,leafmtype,leafdata);CHKERRQ(ierr); } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"PetscSFBcastToZero_Private is not supported on this SF type"); ierr = PetscLogEventEnd(PETSCSF_BcastAndOpBegin,sf,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); }