PetscErrorCode DMPlexPreallocateOperator_2(DM dm, PetscInt bs, PetscSection section, PetscSection sectionGlobal, PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[], Mat A, PetscBool fillMatrix) { PetscInt *tmpClosure,*tmpAdj,*visits; PetscInt c,cStart,cEnd,pStart,pEnd; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); maxClosureSize = 2*PetscMax(PetscPowInt(mesh->maxConeSize,depth+1),PetscPowInt(mesh->maxSupportSize,depth+1)); ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); npoints = pEnd - pStart; ierr = PetscMalloc3(maxClosureSize,&tmpClosure,npoints,&lvisits,npoints,&visits);CHKERRQ(ierr); ierr = PetscMemzero(lvisits,(pEnd-pStart)*sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscMemzero(visits,(pEnd-pStart)*sizeof(PetscInt));CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); for (c=cStart; c<cEnd; c++) { PetscInt *support = tmpClosure; ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_FALSE, &supportSize, (PetscInt**)&support);CHKERRQ(ierr); for (p=0; p<supportSize; p++) lvisits[support[p]]++; } ierr = PetscSFReduceBegin(sf,MPIU_INT,lvisits,visits,MPI_SUM);CHKERRQ(ierr); ierr = PetscSFReduceEnd (sf,MPIU_INT,lvisits,visits,MPI_SUM);CHKERRQ(ierr); ierr = PetscSFBcastBegin(sf,MPIU_INT,visits,lvisits);CHKERRQ(ierr); ierr = PetscSFBcastEnd (sf,MPIU_INT,visits,lvisits);CHKERRQ(ierr); ierr = PetscSFGetRanks();CHKERRQ(ierr); ierr = PetscMalloc2(maxClosureSize*maxClosureSize,&cellmat,npoints,&owner);CHKERRQ(ierr); for (c=cStart; c<cEnd; c++) { ierr = PetscMemzero(cellmat,maxClosureSize*maxClosureSize*sizeof(PetscInt));CHKERRQ(ierr); /* Depth-first walk of transitive closure. At each leaf frame f of transitive closure that we see, add 1/visits[f] to each pair (p,q) not marked as done in cellmat. This contribution is added to dnz if owning ranks of p and q match, to onz otherwise. */ } ierr = PetscSFReduceBegin(sf,MPIU_INT,ldnz,dnz,MPI_SUM);CHKERRQ(ierr); ierr = PetscSFReduceEnd (sf,MPIU_INT,lonz,onz,MPI_SUM);CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode FindCompatibleProblemSize(PetscMPIInt nranks,PetscInt targetlocal,PetscInt size[3]) { PetscErrorCode ierr; PetscInt plev,pgrid[3]; int64_t best = -1; PetscFunctionBegin; for (PetscInt i=0; i<3; i++) size[i] = -1; // We need our computational grids to have at least as many levels as the process grids ierr = ProcessGridFindSquarest(nranks,pgrid);CHKERRQ(ierr); plev = ProcessGridNumLevels(pgrid); for (PetscInt i=0; i<_n_coarse_grids; i++) { const PetscInt *c = _coarse_grids[i]; for (int64_t gsize = (int64_t)c[0]*c[1]*c[2]*PetscPowInt(8,plev),lev=plev; gsize < (int64_t)targetlocal*nranks; gsize *= 8,lev++) { if (gsize > best) { best = gsize; for (PetscInt j=0; j<3; j++) size[j] = c[j] * PetscPowInt(2,lev); } } } PetscFunctionReturn(0); }
PetscErrorCode DMPlexGetAdjacency_Internal(DM dm, PetscInt p, PetscBool useCone, PetscBool useTransitiveClosure, PetscInt *adjSize, PetscInt *adj[]) { static PetscInt asiz = 0; PetscErrorCode ierr; PetscFunctionBeginHot; if (!*adj) { PetscInt depth, maxConeSize, maxSupportSize; ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); asiz = PetscPowInt(maxConeSize, depth+1) * PetscPowInt(maxSupportSize, depth+1) + 1; ierr = PetscMalloc1(asiz,adj);CHKERRQ(ierr); } if (*adjSize < 0) *adjSize = asiz; if (useTransitiveClosure) { ierr = DMPlexGetAdjacency_Transitive_Internal(dm, p, useCone, adjSize, *adj);CHKERRQ(ierr); } else if (useCone) { ierr = DMPlexGetAdjacency_Cone_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); } else { ierr = DMPlexGetAdjacency_Support_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); } PetscFunctionReturn(0); }
static PetscErrorCode MatPartitioningApply_PTScotch_Private(MatPartitioning part, PetscBool useND, IS *partitioning) { MPI_Comm pcomm,comm; MatPartitioning_PTScotch *scotch = (MatPartitioning_PTScotch*)part->data; PetscErrorCode ierr; PetscMPIInt rank; Mat mat = part->adj; Mat_MPIAdj *adj = (Mat_MPIAdj*)mat->data; PetscBool flg,distributed; PetscBool proc_weight_flg; PetscInt i,j,p,bs=1,nold; PetscInt *NDorder = NULL; PetscReal *vwgttab,deltval; SCOTCH_Num *locals,*velotab,*veloloctab,*edloloctab,vertlocnbr,edgelocnbr,nparts=part->n; PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject)part,&pcomm);CHKERRQ(ierr); /* Duplicate the communicator to be sure that PTSCOTCH attribute caching does not interfere with PETSc. */ ierr = MPI_Comm_dup(pcomm,&comm);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)mat,MATMPIADJ,&flg);CHKERRQ(ierr); if (!flg) { /* bs indicates if the converted matrix is "reduced" from the original and hence the resulting partition results need to be stretched to match the original matrix */ nold = mat->rmap->n; ierr = MatConvert(mat,MATMPIADJ,MAT_INITIAL_MATRIX,&mat);CHKERRQ(ierr); if (mat->rmap->n > 0) bs = nold/mat->rmap->n; adj = (Mat_MPIAdj*)mat->data; } proc_weight_flg = PETSC_TRUE; ierr = PetscOptionsGetBool(NULL, NULL, "-mat_partitioning_ptscotch_proc_weight", &proc_weight_flg, NULL);CHKERRQ(ierr); ierr = PetscMalloc1(mat->rmap->n+1,&locals);CHKERRQ(ierr); if (useND) { #if defined(PETSC_HAVE_SCOTCH_PARMETIS_V3_NODEND) PetscInt *sizes, *seps, log2size, subd, *level, base = 0; PetscMPIInt size; ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); log2size = PetscLog2Real(size); subd = PetscPowInt(2,log2size); if (subd != size) SETERRQ(comm,PETSC_ERR_SUP,"Only power of 2 communicator sizes"); ierr = PetscMalloc1(mat->rmap->n,&NDorder);CHKERRQ(ierr); ierr = PetscMalloc3(2*size,&sizes,4*size,&seps,size,&level);CHKERRQ(ierr); SCOTCH_ParMETIS_V3_NodeND(mat->rmap->range,adj->i,adj->j,&base,NULL,NDorder,sizes,&comm); ierr = MatPartitioningSizesToSep_Private(subd,sizes,seps,level);CHKERRQ(ierr); for (i=0;i<mat->rmap->n;i++) { PetscInt loc; ierr = PetscFindInt(NDorder[i],2*subd,seps,&loc);CHKERRQ(ierr); if (loc < 0) { loc = -(loc+1); if (loc%2) { /* part of subdomain */ locals[i] = loc/2; } else { ierr = PetscFindInt(NDorder[i],2*(subd-1),seps+2*subd,&loc);CHKERRQ(ierr); loc = loc < 0 ? -(loc+1)/2 : loc/2; locals[i] = level[loc]; } } else locals[i] = loc/2; } ierr = PetscFree3(sizes,seps,level);CHKERRQ(ierr); #else SETERRQ(pcomm,PETSC_ERR_SUP,"Need libptscotchparmetis.a compiled with -DSCOTCH_METIS_PREFIX"); #endif } else { velotab = NULL; if (proc_weight_flg) { ierr = PetscMalloc1(nparts,&vwgttab);CHKERRQ(ierr); ierr = PetscMalloc1(nparts,&velotab);CHKERRQ(ierr); for (j=0; j<nparts; j++) { if (part->part_weights) vwgttab[j] = part->part_weights[j]*nparts; else vwgttab[j] = 1.0; } for (i=0; i<nparts; i++) { deltval = PetscAbsReal(vwgttab[i]-PetscFloorReal(vwgttab[i]+0.5)); if (deltval>0.01) { for (j=0; j<nparts; j++) vwgttab[j] /= deltval; } } for (i=0; i<nparts; i++) velotab[i] = (SCOTCH_Num)(vwgttab[i] + 0.5); ierr = PetscFree(vwgttab);CHKERRQ(ierr); } vertlocnbr = mat->rmap->range[rank+1] - mat->rmap->range[rank]; edgelocnbr = adj->i[vertlocnbr]; veloloctab = part->vertex_weights; edloloctab = adj->values; /* detect whether all vertices are located at the same process in original graph */ for (p = 0; !mat->rmap->range[p+1] && p < nparts; ++p); distributed = (mat->rmap->range[p+1] == mat->rmap->N) ? PETSC_FALSE : PETSC_TRUE; if (distributed) { SCOTCH_Arch archdat; SCOTCH_Dgraph grafdat; SCOTCH_Dmapping mappdat; SCOTCH_Strat stradat; ierr = SCOTCH_dgraphInit(&grafdat,comm);CHKERRQ(ierr); ierr = SCOTCH_dgraphBuild(&grafdat,0,vertlocnbr,vertlocnbr,adj->i,adj->i+1,veloloctab, NULL,edgelocnbr,edgelocnbr,adj->j,NULL,edloloctab);CHKERRQ(ierr); #if defined(PETSC_USE_DEBUG) ierr = SCOTCH_dgraphCheck(&grafdat);CHKERRQ(ierr); #endif ierr = SCOTCH_archInit(&archdat);CHKERRQ(ierr); ierr = SCOTCH_stratInit(&stradat);CHKERRQ(ierr); ierr = SCOTCH_stratDgraphMapBuild(&stradat,scotch->strategy,nparts,nparts,scotch->imbalance);CHKERRQ(ierr); if (velotab) { ierr = SCOTCH_archCmpltw(&archdat,nparts,velotab);CHKERRQ(ierr); } else { ierr = SCOTCH_archCmplt( &archdat,nparts);CHKERRQ(ierr); } ierr = SCOTCH_dgraphMapInit(&grafdat,&mappdat,&archdat,locals);CHKERRQ(ierr); ierr = SCOTCH_dgraphMapCompute(&grafdat,&mappdat,&stradat);CHKERRQ(ierr); SCOTCH_dgraphMapExit(&grafdat,&mappdat); SCOTCH_archExit(&archdat); SCOTCH_stratExit(&stradat); SCOTCH_dgraphExit(&grafdat); } else if (rank == p) { SCOTCH_Graph grafdat; SCOTCH_Strat stradat; ierr = SCOTCH_graphInit(&grafdat);CHKERRQ(ierr); ierr = SCOTCH_graphBuild(&grafdat,0,vertlocnbr,adj->i,adj->i+1,veloloctab,NULL,edgelocnbr,adj->j,edloloctab);CHKERRQ(ierr); #if defined(PETSC_USE_DEBUG) ierr = SCOTCH_graphCheck(&grafdat);CHKERRQ(ierr); #endif ierr = SCOTCH_stratInit(&stradat);CHKERRQ(ierr); ierr = SCOTCH_stratGraphMapBuild(&stradat,scotch->strategy,nparts,scotch->imbalance);CHKERRQ(ierr); ierr = SCOTCH_graphPart(&grafdat,nparts,&stradat,locals);CHKERRQ(ierr); SCOTCH_stratExit(&stradat); SCOTCH_graphExit(&grafdat); } ierr = PetscFree(velotab);CHKERRQ(ierr); } ierr = MPI_Comm_free(&comm);CHKERRQ(ierr); if (bs > 1) { PetscInt *newlocals; ierr = PetscMalloc1(bs*mat->rmap->n,&newlocals);CHKERRQ(ierr); for (i=0;i<mat->rmap->n;i++) { for (j=0;j<bs;j++) { newlocals[bs*i+j] = locals[i]; } } ierr = PetscFree(locals);CHKERRQ(ierr); ierr = ISCreateGeneral(pcomm,bs*mat->rmap->n,newlocals,PETSC_OWN_POINTER,partitioning);CHKERRQ(ierr); } else { ierr = ISCreateGeneral(pcomm,mat->rmap->n,locals,PETSC_OWN_POINTER,partitioning);CHKERRQ(ierr); } if (useND) { IS ndis; if (bs > 1) { ierr = ISCreateBlock(pcomm,bs,mat->rmap->n,NDorder,PETSC_OWN_POINTER,&ndis);CHKERRQ(ierr); } else { ierr = ISCreateGeneral(pcomm,mat->rmap->n,NDorder,PETSC_OWN_POINTER,&ndis);CHKERRQ(ierr); } ierr = ISSetPermutation(ndis);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject)(*partitioning),"_petsc_matpartitioning_ndorder",(PetscObject)ndis);CHKERRQ(ierr); ierr = ISDestroy(&ndis);CHKERRQ(ierr); } if (!flg) { ierr = MatDestroy(&mat);CHKERRQ(ierr); } PetscFunctionReturn(0); }
static PetscErrorCode MatPartitioningApply_Parmetis_Private(MatPartitioning part, PetscBool useND, IS *partitioning) { MatPartitioning_Parmetis *pmetis = (MatPartitioning_Parmetis*)part->data; PetscErrorCode ierr; PetscInt *locals = NULL; Mat mat = part->adj,amat,pmat; PetscBool flg; PetscInt bs = 1; PetscFunctionBegin; ierr = PetscObjectTypeCompare((PetscObject)mat,MATMPIADJ,&flg);CHKERRQ(ierr); if (flg) { amat = mat; ierr = PetscObjectReference((PetscObject)amat);CHKERRQ(ierr); } else { /* bs indicates if the converted matrix is "reduced" from the original and hence the resulting partition results need to be stretched to match the original matrix */ ierr = MatConvert(mat,MATMPIADJ,MAT_INITIAL_MATRIX,&amat);CHKERRQ(ierr); if (amat->rmap->n > 0) bs = mat->rmap->n/amat->rmap->n; } ierr = MatMPIAdjCreateNonemptySubcommMat(amat,&pmat);CHKERRQ(ierr); ierr = MPI_Barrier(PetscObjectComm((PetscObject)part));CHKERRQ(ierr); if (pmat) { MPI_Comm pcomm,comm; Mat_MPIAdj *adj = (Mat_MPIAdj*)pmat->data; PetscInt *vtxdist = pmat->rmap->range; PetscInt *xadj = adj->i; PetscInt *adjncy = adj->j; PetscInt *NDorder = NULL; PetscInt itmp = 0,wgtflag=0, numflag=0, ncon=1, nparts=part->n, options[24], i, j; real_t *tpwgts,*ubvec,itr=0.1; int status; ierr = PetscObjectGetComm((PetscObject)pmat,&pcomm);CHKERRQ(ierr); #if defined(PETSC_USE_DEBUG) /* check that matrix has no diagonal entries */ { PetscInt rstart; ierr = MatGetOwnershipRange(pmat,&rstart,NULL);CHKERRQ(ierr); for (i=0; i<pmat->rmap->n; i++) { for (j=xadj[i]; j<xadj[i+1]; j++) { if (adjncy[j] == i+rstart) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Row %d has diagonal entry; Parmetis forbids diagonal entry",i+rstart); } } } #endif ierr = PetscMalloc1(pmat->rmap->n,&locals);CHKERRQ(ierr); if (adj->values && !part->vertex_weights) wgtflag = 1; if (part->vertex_weights && !adj->values) wgtflag = 2; if (part->vertex_weights && adj->values) wgtflag = 3; if (PetscLogPrintInfo) {itmp = pmetis->printout; pmetis->printout = 127;} ierr = PetscMalloc1(ncon*nparts,&tpwgts);CHKERRQ(ierr); for (i=0; i<ncon; i++) { for (j=0; j<nparts; j++) { if (part->part_weights) { tpwgts[i*nparts+j] = part->part_weights[i*nparts+j]; } else { tpwgts[i*nparts+j] = 1./nparts; } } } ierr = PetscMalloc1(ncon,&ubvec);CHKERRQ(ierr); for (i=0; i<ncon; i++) { ubvec[i] = 1.05; } /* This sets the defaults */ options[0] = 0; for (i=1; i<24; i++) { options[i] = -1; } /* Duplicate the communicator to be sure that ParMETIS attribute caching does not interfere with PETSc. */ ierr = MPI_Comm_dup(pcomm,&comm);CHKERRQ(ierr); if (useND) { PetscInt *sizes, *seps, log2size, subd, *level; PetscMPIInt size; idx_t mtype = PARMETIS_MTYPE_GLOBAL, rtype = PARMETIS_SRTYPE_2PHASE, p_nseps = 1, s_nseps = 1; real_t ubfrac = 1.05; ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); ierr = PetscMalloc1(pmat->rmap->n,&NDorder);CHKERRQ(ierr); ierr = PetscMalloc3(2*size,&sizes,4*size,&seps,size,&level);CHKERRQ(ierr); PetscStackCallParmetis(ParMETIS_V32_NodeND,((idx_t*)vtxdist,(idx_t*)xadj,(idx_t*)adjncy,(idx_t*)part->vertex_weights,(idx_t*)&numflag,&mtype,&rtype,&p_nseps,&s_nseps,&ubfrac,NULL/* seed */,NULL/* dbglvl */,(idx_t*)NDorder,(idx_t*)(sizes),&comm)); log2size = PetscLog2Real(size); subd = PetscPowInt(2,log2size); ierr = MatPartitioningSizesToSep_Private(subd,sizes,seps,level);CHKERRQ(ierr); for (i=0;i<pmat->rmap->n;i++) { PetscInt loc; ierr = PetscFindInt(NDorder[i],2*subd,seps,&loc);CHKERRQ(ierr); if (loc < 0) { loc = -(loc+1); if (loc%2) { /* part of subdomain */ locals[i] = loc/2; } else { ierr = PetscFindInt(NDorder[i],2*(subd-1),seps+2*subd,&loc);CHKERRQ(ierr); loc = loc < 0 ? -(loc+1)/2 : loc/2; locals[i] = level[loc]; } } else locals[i] = loc/2; } ierr = PetscFree3(sizes,seps,level);CHKERRQ(ierr); } else { if (pmetis->repartition) { PetscStackCallParmetis(ParMETIS_V3_AdaptiveRepart,((idx_t*)vtxdist,(idx_t*)xadj,(idx_t*)adjncy,(idx_t*)part->vertex_weights,(idx_t*)part->vertex_weights,(idx_t*)adj->values,(idx_t*)&wgtflag,(idx_t*)&numflag,(idx_t*)&ncon,(idx_t*)&nparts,tpwgts,ubvec,&itr,(idx_t*)options,(idx_t*)&pmetis->cuts,(idx_t*)locals,&comm)); } else { PetscStackCallParmetis(ParMETIS_V3_PartKway,((idx_t*)vtxdist,(idx_t*)xadj,(idx_t*)adjncy,(idx_t*)part->vertex_weights,(idx_t*)adj->values,(idx_t*)&wgtflag,(idx_t*)&numflag,(idx_t*)&ncon,(idx_t*)&nparts,tpwgts,ubvec,(idx_t*)options,(idx_t*)&pmetis->cuts,(idx_t*)locals,&comm)); } } ierr = MPI_Comm_free(&comm);CHKERRQ(ierr); ierr = PetscFree(tpwgts);CHKERRQ(ierr); ierr = PetscFree(ubvec);CHKERRQ(ierr); if (PetscLogPrintInfo) pmetis->printout = itmp; if (bs > 1) { PetscInt i,j,*newlocals; ierr = PetscMalloc1(bs*pmat->rmap->n,&newlocals);CHKERRQ(ierr); for (i=0; i<pmat->rmap->n; i++) { for (j=0; j<bs; j++) { newlocals[bs*i + j] = locals[i]; } } ierr = PetscFree(locals);CHKERRQ(ierr); ierr = ISCreateGeneral(PetscObjectComm((PetscObject)part),bs*pmat->rmap->n,newlocals,PETSC_OWN_POINTER,partitioning);CHKERRQ(ierr); } else { ierr = ISCreateGeneral(PetscObjectComm((PetscObject)part),pmat->rmap->n,locals,PETSC_OWN_POINTER,partitioning);CHKERRQ(ierr); } if (useND) { IS ndis; if (bs > 1) { ierr = ISCreateBlock(PetscObjectComm((PetscObject)part),bs,pmat->rmap->n,NDorder,PETSC_OWN_POINTER,&ndis);CHKERRQ(ierr); } else { ierr = ISCreateGeneral(PetscObjectComm((PetscObject)part),pmat->rmap->n,NDorder,PETSC_OWN_POINTER,&ndis);CHKERRQ(ierr); } ierr = ISSetPermutation(ndis);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject)(*partitioning),"_petsc_matpartitioning_ndorder",(PetscObject)ndis);CHKERRQ(ierr); ierr = ISDestroy(&ndis);CHKERRQ(ierr); } } else { ierr = ISCreateGeneral(PetscObjectComm((PetscObject)part),0,NULL,PETSC_COPY_VALUES,partitioning);CHKERRQ(ierr); if (useND) { IS ndis; if (bs > 1) { ierr = ISCreateBlock(PetscObjectComm((PetscObject)part),bs,0,NULL,PETSC_COPY_VALUES,&ndis);CHKERRQ(ierr); } else { ierr = ISCreateGeneral(PetscObjectComm((PetscObject)part),0,NULL,PETSC_COPY_VALUES,&ndis);CHKERRQ(ierr); } ierr = ISSetPermutation(ndis);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject)(*partitioning),"_petsc_matpartitioning_ndorder",(PetscObject)ndis);CHKERRQ(ierr); ierr = ISDestroy(&ndis);CHKERRQ(ierr); } } ierr = MatDestroy(&pmat);CHKERRQ(ierr); ierr = MatDestroy(&amat);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc, char **argv) { DM dm; PetscSection s; Vec u; AppCtx user; PetscInt cells[3] = {2, 2, 2}; PetscInt size = 0, cStart, cEnd, cell, c, f, i, j; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); ierr = DMPlexCreateHexBoxMesh(PETSC_COMM_WORLD, user.dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr); ierr = DMSetFromOptions(dm);CHKERRQ(ierr); /* Create a section for SEM order k */ { PetscInt *numDof, d; ierr = PetscMalloc1(user.Nf*(user.dim+1), &numDof);CHKERRQ(ierr); for (f = 0; f < user.Nf; ++f) { for (d = 0; d <= user.dim; ++d) numDof[f*(user.dim+1)+d] = PetscPowInt(user.k[f]-1, d)*user.Nc[f]; size += PetscPowInt(user.k[f]+1, d)*user.Nc[f]; } ierr = DMPlexCreateSection(dm, user.dim, user.Nf, user.Nc, numDof, 0, NULL, NULL, NULL, NULL, &s);CHKERRQ(ierr); ierr = SetSymmetries(dm, s, &user);CHKERRQ(ierr); ierr = PetscFree(numDof);CHKERRQ(ierr); } ierr = DMSetDefaultSection(dm, s);CHKERRQ(ierr); /* Create spectral ordering and load in data */ ierr = DMPlexCreateSpectralClosurePermutation(dm, NULL);CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &u);CHKERRQ(ierr); switch (user.dim) { case 2: ierr = LoadData2D(dm, 2, 2, size, u, &user);CHKERRQ(ierr);break; case 3: ierr = LoadData3D(dm, 2, 2, 2, size, u, &user);CHKERRQ(ierr);break; } /* Remove ordering and check some values */ ierr = PetscSectionSetClosurePermutation(s, (PetscObject) dm, NULL);CHKERRQ(ierr); switch (user.dim) { case 2: ierr = CheckPoint(dm, u, 0, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 13, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 15, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 19, &user);CHKERRQ(ierr); break; case 3: ierr = CheckPoint(dm, u, 0, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 13, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 15, &user);CHKERRQ(ierr); ierr = CheckPoint(dm, u, 19, &user);CHKERRQ(ierr); break; } /* Recreate spectral ordering and read out data */ ierr = DMPlexCreateSpectralClosurePermutation(dm, s);CHKERRQ(ierr); switch (user.dim) { case 2: ierr = ReadData2D(dm, u, &user);CHKERRQ(ierr);break; case 3: ierr = ReadData3D(dm, u, &user);CHKERRQ(ierr);break; } ierr = DMRestoreLocalVector(dm, &u);CHKERRQ(ierr); ierr = PetscSectionDestroy(&s);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFree(user.Nc);CHKERRQ(ierr); ierr = PetscFree(user.k);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode DMPlexGetAdjacency_Internal(DM dm, PetscInt p, PetscBool useCone, PetscBool useTransitiveClosure, PetscBool useAnchors, PetscInt *adjSize, PetscInt *adj[]) { static PetscInt asiz = 0; PetscInt maxAnchors = 1; PetscInt aStart = -1, aEnd = -1; PetscInt maxAdjSize; PetscSection aSec = NULL; IS aIS = NULL; const PetscInt *anchors; PetscErrorCode ierr; PetscFunctionBeginHot; if (useAnchors) { ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr); if (aSec) { ierr = PetscSectionGetMaxDof(aSec,&maxAnchors);CHKERRQ(ierr); maxAnchors = PetscMax(1,maxAnchors); ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr); ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); } } if (!*adj) { PetscInt depth, coneSeries, supportSeries, maxC, maxS, pStart, pEnd; ierr = DMPlexGetChart(dm, &pStart,&pEnd);CHKERRQ(ierr); ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetMaxSizes(dm, &maxC, &maxS);CHKERRQ(ierr); coneSeries = (maxC > 1) ? ((PetscPowInt(maxC,depth+1)-1)/(maxC-1)) : depth+1; supportSeries = (maxS > 1) ? ((PetscPowInt(maxS,depth+1)-1)/(maxS-1)) : depth+1; asiz = PetscMax(PetscPowInt(maxS,depth)*coneSeries,PetscPowInt(maxC,depth)*supportSeries); asiz *= maxAnchors; asiz = PetscMin(asiz,pEnd-pStart); ierr = PetscMalloc1(asiz,adj);CHKERRQ(ierr); } if (*adjSize < 0) *adjSize = asiz; maxAdjSize = *adjSize; if (useTransitiveClosure) { ierr = DMPlexGetAdjacency_Transitive_Internal(dm, p, useCone, adjSize, *adj);CHKERRQ(ierr); } else if (useCone) { ierr = DMPlexGetAdjacency_Cone_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); } else { ierr = DMPlexGetAdjacency_Support_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); } if (useAnchors && aSec) { PetscInt origSize = *adjSize; PetscInt numAdj = origSize; PetscInt i = 0, j; PetscInt *orig = *adj; while (i < origSize) { PetscInt p = orig[i]; PetscInt aDof = 0; if (p >= aStart && p < aEnd) { ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); } if (aDof) { PetscInt aOff; PetscInt s, q; for (j = i + 1; j < numAdj; j++) { orig[j - 1] = orig[j]; } origSize--; numAdj--; ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); for (s = 0; s < aDof; ++s) { for (q = 0; q < numAdj || (orig[numAdj++] = anchors[aOff+s],0); ++q) { if (anchors[aOff+s] == orig[q]) break; } if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); } } else { i++; } } *adjSize = numAdj; ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); } PetscFunctionReturn(0); }