static PetscErrorCode DMPlexVTKWriteAll_ASCII(DM dm, PetscViewer viewer) { MPI_Comm comm; PetscViewer_VTK *vtk = (PetscViewer_VTK*) viewer->data; FILE *fp; PetscViewerVTKObjectLink link; PetscSection coordSection, globalCoordSection; PetscLayout vLayout; Vec coordinates; PetscReal lengthScale; PetscInt vMax, totVertices, totCells; PetscBool hasPoint = PETSC_FALSE, hasCell = PETSC_FALSE, writePartition = PETSC_FALSE; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); ierr = PetscFOpen(comm, vtk->filename, "wb", &fp);CHKERRQ(ierr); ierr = PetscFPrintf(comm, fp, "# vtk DataFile Version 2.0\n");CHKERRQ(ierr); ierr = PetscFPrintf(comm, fp, "Simplicial Mesh Example\n");CHKERRQ(ierr); ierr = PetscFPrintf(comm, fp, "ASCII\n");CHKERRQ(ierr); ierr = PetscFPrintf(comm, fp, "DATASET UNSTRUCTURED_GRID\n");CHKERRQ(ierr); /* Vertices */ ierr = DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);CHKERRQ(ierr); ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionCreateGlobalSection(coordSection, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalCoordSection);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, NULL, NULL, NULL, &vMax);CHKERRQ(ierr); if (vMax >= 0) { PetscInt pStart, pEnd, p, localSize = 0; ierr = PetscSectionGetChart(globalCoordSection, &pStart, &pEnd);CHKERRQ(ierr); pEnd = PetscMin(pEnd, vMax); for (p = pStart; p < pEnd; ++p) { PetscInt dof; ierr = PetscSectionGetDof(globalCoordSection, p, &dof);CHKERRQ(ierr); if (dof > 0) ++localSize; } ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &vLayout);CHKERRQ(ierr); ierr = PetscLayoutSetLocalSize(vLayout, localSize);CHKERRQ(ierr); ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); } else { ierr = PetscSectionGetPointLayout(PetscObjectComm((PetscObject)dm), globalCoordSection, &vLayout);CHKERRQ(ierr); } ierr = PetscLayoutGetSize(vLayout, &totVertices);CHKERRQ(ierr); ierr = PetscFPrintf(comm, fp, "POINTS %d double\n", totVertices);CHKERRQ(ierr); ierr = DMPlexVTKWriteSection_ASCII(dm, coordSection, globalCoordSection, coordinates, fp, 3, PETSC_DETERMINE, lengthScale);CHKERRQ(ierr); /* Cells */ ierr = DMPlexVTKWriteCells_ASCII(dm, fp, &totCells);CHKERRQ(ierr); /* Vertex fields */ for (link = vtk->link; link; link = link->next) { if ((link->ft == PETSC_VTK_POINT_FIELD) || (link->ft == PETSC_VTK_POINT_VECTOR_FIELD)) hasPoint = PETSC_TRUE; if ((link->ft == PETSC_VTK_CELL_FIELD) || (link->ft == PETSC_VTK_CELL_VECTOR_FIELD)) hasCell = PETSC_TRUE; } if (hasPoint) { ierr = PetscFPrintf(comm, fp, "POINT_DATA %d\n", totVertices);CHKERRQ(ierr); for (link = vtk->link; link; link = link->next) { Vec X = (Vec) link->vec; DM dmX; PetscSection section, globalSection, newSection = NULL; const char *name; PetscInt enforceDof = PETSC_DETERMINE; if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue; if (link->ft == PETSC_VTK_POINT_VECTOR_FIELD) enforceDof = 3; ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr); ierr = VecGetDM(X, &dmX);CHKERRQ(ierr); if (dmX) { DMLabel subpointMap, subpointMapX; PetscInt dim, dimX, pStart, pEnd, qStart, qEnd; ierr = DMGetDefaultSection(dmX, §ion);CHKERRQ(ierr); /* Here is where we check whether dmX is a submesh of dm */ ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetDimension(dmX, &dimX);CHKERRQ(ierr); ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); ierr = DMPlexGetChart(dmX, &qStart, &qEnd);CHKERRQ(ierr); ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr); ierr = DMPlexGetSubpointMap(dmX, &subpointMapX);CHKERRQ(ierr); if (((dim != dimX) || ((pEnd-pStart) < (qEnd-qStart))) && subpointMap && !subpointMapX) { const PetscInt *ind = NULL; IS subpointIS; PetscInt n = 0, q; ierr = PetscSectionGetChart(section, &qStart, &qEnd);CHKERRQ(ierr); ierr = DMPlexCreateSubpointIS(dm, &subpointIS);CHKERRQ(ierr); if (subpointIS) { ierr = ISGetLocalSize(subpointIS, &n);CHKERRQ(ierr); ierr = ISGetIndices(subpointIS, &ind);CHKERRQ(ierr); } ierr = PetscSectionCreate(comm, &newSection);CHKERRQ(ierr); ierr = PetscSectionSetChart(newSection, pStart, pEnd);CHKERRQ(ierr); for (q = qStart; q < qEnd; ++q) { PetscInt dof, off, p; ierr = PetscSectionGetDof(section, q, &dof);CHKERRQ(ierr); if (dof) { ierr = PetscFindInt(q, n, ind, &p);CHKERRQ(ierr); if (p >= pStart) { ierr = PetscSectionSetDof(newSection, p, dof);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, q, &off);CHKERRQ(ierr); ierr = PetscSectionSetOffset(newSection, p, off);CHKERRQ(ierr); } } } if (subpointIS) { ierr = ISRestoreIndices(subpointIS, &ind);CHKERRQ(ierr); ierr = ISDestroy(&subpointIS);CHKERRQ(ierr); } /* No need to setup section */ section = newSection; } } else { ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) §ion);CHKERRQ(ierr); if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name); } if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name); ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr); ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr); ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr); if (newSection) {ierr = PetscSectionDestroy(&newSection);CHKERRQ(ierr);} } } /* Cell Fields */ ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_view_partition", &writePartition, NULL);CHKERRQ(ierr); if (hasCell || writePartition) { ierr = PetscFPrintf(comm, fp, "CELL_DATA %d\n", totCells);CHKERRQ(ierr); for (link = vtk->link; link; link = link->next) { Vec X = (Vec) link->vec; DM dmX; PetscSection section, globalSection; const char *name; PetscInt enforceDof = PETSC_DETERMINE; if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue; if (link->ft == PETSC_VTK_CELL_VECTOR_FIELD) enforceDof = 3; ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr); ierr = VecGetDM(X, &dmX);CHKERRQ(ierr); if (dmX) { ierr = DMGetDefaultSection(dmX, §ion);CHKERRQ(ierr); } else { PetscContainer c; ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) &c);CHKERRQ(ierr); if (!c) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name); ierr = PetscContainerGetPointer(c, (void**) §ion);CHKERRQ(ierr); } if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name); ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr); ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr); ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr); } if (writePartition) { ierr = PetscFPrintf(comm, fp, "SCALARS partition int 1\n");CHKERRQ(ierr); ierr = PetscFPrintf(comm, fp, "LOOKUP_TABLE default\n");CHKERRQ(ierr); ierr = DMPlexVTKWritePartition_ASCII(dm, fp);CHKERRQ(ierr); } } /* Cleanup */ ierr = PetscSectionDestroy(&globalCoordSection);CHKERRQ(ierr); ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); ierr = PetscFClose(comm, fp);CHKERRQ(ierr); PetscFunctionReturn(0); }
/*@ DMPlexGetOrdering - Calculate a reordering of the mesh Collective on DM Input Parameter: + dm - The DMPlex object . otype - type of reordering, one of the following: $ MATORDERINGNATURAL - Natural $ MATORDERINGND - Nested Dissection $ MATORDERING1WD - One-way Dissection $ MATORDERINGRCM - Reverse Cuthill-McKee $ MATORDERINGQMD - Quotient Minimum Degree - label - [Optional] Label used to segregate ordering into sets, or NULL Output Parameter: . perm - The point permutation as an IS, perm[old point number] = new point number Note: The label is used to group sets of points together by label value. This makes it easy to reorder a mesh which has different types of cells, and then loop over each set of reordered cells for assembly. Level: intermediate .keywords: mesh .seealso: MatGetOrdering() @*/ PetscErrorCode DMPlexGetOrdering(DM dm, MatOrderingType otype, DMLabel label, IS *perm) { PetscInt numCells = 0; PetscInt *start = NULL, *adjacency = NULL, *cperm, *clperm, *invclperm, *mask, *xls, pStart, pEnd, c, i; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); PetscValidPointer(perm, 3); ierr = DMPlexCreateNeighborCSR(dm, 0, &numCells, &start, &adjacency);CHKERRQ(ierr); ierr = PetscMalloc3(numCells,&cperm,numCells,&mask,numCells*2,&xls);CHKERRQ(ierr); if (numCells) { /* Shift for Fortran numbering */ for (i = 0; i < start[numCells]; ++i) ++adjacency[i]; for (i = 0; i <= numCells; ++i) ++start[i]; ierr = SPARSEPACKgenrcm(&numCells, start, adjacency, cperm, mask, xls);CHKERRQ(ierr); } ierr = PetscFree(start);CHKERRQ(ierr); ierr = PetscFree(adjacency);CHKERRQ(ierr); /* Shift for Fortran numbering */ for (c = 0; c < numCells; ++c) --cperm[c]; /* Segregate */ if (label) { IS valueIS; const PetscInt *values; PetscInt numValues, numPoints = 0; PetscInt *sperm, *vsize, *voff, v; ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); ierr = ISSort(valueIS);CHKERRQ(ierr); ierr = ISGetLocalSize(valueIS, &numValues);CHKERRQ(ierr); ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); ierr = PetscCalloc3(numCells,&sperm,numValues,&vsize,numValues+1,&voff);CHKERRQ(ierr); for (v = 0; v < numValues; ++v) { ierr = DMLabelGetStratumSize(label, values[v], &vsize[v]);CHKERRQ(ierr); if (v < numValues-1) voff[v+2] += vsize[v] + voff[v+1]; numPoints += vsize[v]; } if (numPoints != numCells) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Label only covers %D cells < %D total", numPoints, numCells); for (c = 0; c < numCells; ++c) { const PetscInt oldc = cperm[c]; PetscInt val, vloc; ierr = DMLabelGetValue(label, oldc, &val);CHKERRQ(ierr); if (val == -1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cell %D not present in label", oldc); ierr = PetscFindInt(val, numValues, values, &vloc);CHKERRQ(ierr); if (vloc < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Value %D not present label", val); sperm[voff[vloc+1]++] = oldc; } for (v = 0; v < numValues; ++v) { if (voff[v+1] - voff[v] != vsize[v]) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of %D values found is %D != %D", values[v], voff[v+1] - voff[v], vsize[v]); } ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); ierr = ISDestroy(&valueIS);CHKERRQ(ierr); ierr = PetscMemcpy(cperm, sperm, numCells * sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscFree3(sperm, vsize, voff);CHKERRQ(ierr); } /* Construct closure */ ierr = DMPlexCreateOrderingClosure_Static(dm, numCells, cperm, &clperm, &invclperm);CHKERRQ(ierr); ierr = PetscFree3(cperm,mask,xls);CHKERRQ(ierr); ierr = PetscFree(clperm);CHKERRQ(ierr); /* Invert permutation */ ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); ierr = ISCreateGeneral(PetscObjectComm((PetscObject) dm), pEnd-pStart, invclperm, PETSC_OWN_POINTER, perm);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); }
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); }
/* DMPatchZoom - Create a version of the coarse patch (identified by rank) with halo on communicator commz Collective on DM Input Parameters: + dm - the DM . rank - the rank which holds the given patch - commz - the new communicator for the patch Output Parameters: + dmz - the patch DM . sfz - the PetscSF mapping the patch+halo to the zoomed version . sfzr - the PetscSF mapping the patch to the restricted zoomed version Level: intermediate Note: All processes in commz should have the same rank (could autosplit comm) .seealso: DMPatchSolve() */ PetscErrorCode DMPatchZoom(DM dm, Vec X, MatStencil lower, MatStencil upper, MPI_Comm commz, DM *dmz, PetscSF *sfz, PetscSF *sfzr) { DMDAStencilType st; MatStencil blower, bupper, loclower, locupper; IS is; const PetscInt *ranges, *indices; PetscInt *localPoints = NULL; PetscSFNode *remotePoints = NULL; PetscInt dim, dof; PetscInt M, N, P, rM, rN, rP, halo = 1, sxb, syb, szb, sxr, syr, szr, exr, eyr, ezr, mxb, myb, mzb, i, j, k, q; PetscMPIInt size; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);CHKERRQ(ierr); /* Create patch DM */ ierr = DMDAGetInfo(dm, &dim, &M, &N, &P, 0,0,0, &dof, 0,0,0,0, &st);CHKERRQ(ierr); /* Get piece for rank r, expanded by halo */ bupper.i = PetscMin(M, upper.i + halo); blower.i = PetscMax(lower.i - halo, 0); bupper.j = PetscMin(N, upper.j + halo); blower.j = PetscMax(lower.j - halo, 0); bupper.k = PetscMin(P, upper.k + halo); blower.k = PetscMax(lower.k - halo, 0); rM = bupper.i - blower.i; rN = bupper.j - blower.j; rP = bupper.k - blower.k; if (commz != MPI_COMM_NULL) { ierr = DMDACreate(commz, dmz);CHKERRQ(ierr); ierr = DMSetDimension(*dmz, dim);CHKERRQ(ierr); ierr = DMDASetSizes(*dmz, rM, rN, rP);CHKERRQ(ierr); ierr = DMDASetNumProcs(*dmz, PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE);CHKERRQ(ierr); ierr = DMDASetBoundaryType(*dmz, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE);CHKERRQ(ierr); ierr = DMDASetDof(*dmz, dof);CHKERRQ(ierr); ierr = DMDASetStencilType(*dmz, st);CHKERRQ(ierr); ierr = DMDASetStencilWidth(*dmz, 0);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(*dmz, NULL, NULL, NULL);CHKERRQ(ierr); ierr = DMSetFromOptions(*dmz);CHKERRQ(ierr); ierr = DMSetUp(*dmz);CHKERRQ(ierr); ierr = DMDAGetCorners(*dmz, &sxb, &syb, &szb, &mxb, &myb, &mzb);CHKERRQ(ierr); sxr = PetscMax(sxb, lower.i - blower.i); syr = PetscMax(syb, lower.j - blower.j); szr = PetscMax(szb, lower.k - blower.k); exr = PetscMin(sxb+mxb, upper.i - blower.i); eyr = PetscMin(syb+myb, upper.j - blower.j); ezr = PetscMin(szb+mzb, upper.k - blower.k); ierr = PetscMalloc2(rM*rN*rP,&localPoints,rM*rN*rP,&remotePoints);CHKERRQ(ierr); } else { sxr = syr = szr = exr = eyr = ezr = sxb = syb = szb = mxb = myb = mzb = 0; } /* Create SF for restricted map */ ierr = VecGetOwnershipRanges(X,&ranges);CHKERRQ(ierr); loclower.i = blower.i + sxr; locupper.i = blower.i + exr; loclower.j = blower.j + syr; locupper.j = blower.j + eyr; loclower.k = blower.k + szr; locupper.k = blower.k + ezr; ierr = DMDACreatePatchIS(dm, &loclower, &locupper, &is);CHKERRQ(ierr); ierr = ISGetIndices(is, &indices);CHKERRQ(ierr); q = 0; for (k = szb; k < szb+mzb; ++k) { if ((k < szr) || (k >= ezr)) continue; for (j = syb; j < syb+myb; ++j) { if ((j < syr) || (j >= eyr)) continue; for (i = sxb; i < sxb+mxb; ++i) { const PetscInt lp = ((k-szb)*rN + (j-syb))*rM + i-sxb; PetscInt r; if ((i < sxr) || (i >= exr)) continue; localPoints[q] = lp; ierr = PetscFindInt(indices[q], size+1, ranges, &r);CHKERRQ(ierr); remotePoints[q].rank = r < 0 ? -(r+1) - 1 : r; remotePoints[q].index = indices[q] - ranges[remotePoints[q].rank]; ++q; } } } ierr = ISRestoreIndices(is, &indices);CHKERRQ(ierr); ierr = ISDestroy(&is);CHKERRQ(ierr); ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfzr);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *sfzr, "Restricted Map");CHKERRQ(ierr); ierr = PetscSFSetGraph(*sfzr, M*N*P, q, localPoints, PETSC_COPY_VALUES, remotePoints, PETSC_COPY_VALUES);CHKERRQ(ierr); /* Create SF for buffered map */ loclower.i = blower.i + sxb; locupper.i = blower.i + sxb+mxb; loclower.j = blower.j + syb; locupper.j = blower.j + syb+myb; loclower.k = blower.k + szb; locupper.k = blower.k + szb+mzb; ierr = DMDACreatePatchIS(dm, &loclower, &locupper, &is);CHKERRQ(ierr); ierr = ISGetIndices(is, &indices);CHKERRQ(ierr); q = 0; for (k = szb; k < szb+mzb; ++k) { for (j = syb; j < syb+myb; ++j) { for (i = sxb; i < sxb+mxb; ++i, ++q) { PetscInt r; localPoints[q] = q; ierr = PetscFindInt(indices[q], size+1, ranges, &r);CHKERRQ(ierr); remotePoints[q].rank = r < 0 ? -(r+1) - 1 : r; remotePoints[q].index = indices[q] - ranges[remotePoints[q].rank]; } } } ierr = ISRestoreIndices(is, &indices);CHKERRQ(ierr); ierr = ISDestroy(&is);CHKERRQ(ierr); ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfz);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *sfz, "Buffered Map");CHKERRQ(ierr); ierr = PetscSFSetGraph(*sfz, M*N*P, q, localPoints, PETSC_COPY_VALUES, remotePoints, PETSC_COPY_VALUES);CHKERRQ(ierr); ierr = PetscFree2(localPoints, remotePoints);CHKERRQ(ierr); PetscFunctionReturn(0); }
/* * The interface should be easy to use for both MatGetSubMatrix (parallel sub-matrix) and MatGetSubMatrices (sequential sub-matrices) * */ static PetscErrorCode MatGetSubMatrix_MPIAdj_data(Mat adj,IS irows, IS icols, PetscInt **sadj_xadj,PetscInt **sadj_adjncy,PetscInt **sadj_values) { PetscInt nlrows_is,icols_n,i,j,nroots,nleaves,owner,rlocalindex,*ncols_send,*ncols_recv; PetscInt nlrows_mat,*adjncy_recv,Ncols_recv,Ncols_send,*xadj_recv,*values_recv; PetscInt *ncols_recv_offsets,loc,rnclos,*sadjncy,*sxadj,*svalues,isvalue; const PetscInt *irows_indices,*icols_indices,*xadj, *adjncy; Mat_MPIAdj *a = (Mat_MPIAdj*)adj->data; PetscLayout rmap; MPI_Comm comm; PetscSF sf; PetscSFNode *iremote; PetscBool done; PetscErrorCode ierr; PetscFunctionBegin; /* communicator */ ierr = PetscObjectGetComm((PetscObject)adj,&comm);CHKERRQ(ierr); /* Layouts */ ierr = MatGetLayouts(adj,&rmap,PETSC_NULL);CHKERRQ(ierr); /* get rows information */ ierr = ISGetLocalSize(irows,&nlrows_is);CHKERRQ(ierr); ierr = ISGetIndices(irows,&irows_indices);CHKERRQ(ierr); ierr = PetscCalloc1(nlrows_is,&iremote);CHKERRQ(ierr); /* construct sf graph*/ nleaves = nlrows_is; for(i=0; i<nlrows_is; i++){ owner = -1; rlocalindex = -1; ierr = PetscLayoutFindOwnerIndex(rmap,irows_indices[i],&owner,&rlocalindex);CHKERRQ(ierr); iremote[i].rank = owner; iremote[i].index = rlocalindex; } ierr = MatGetRowIJ(adj,0,PETSC_FALSE,PETSC_FALSE,&nlrows_mat,&xadj,&adjncy,&done);CHKERRQ(ierr); ierr = PetscCalloc4(nlrows_mat,&ncols_send,nlrows_is,&xadj_recv,nlrows_is+1,&ncols_recv_offsets,nlrows_is,&ncols_recv);CHKERRQ(ierr); nroots = nlrows_mat; for(i=0; i<nlrows_mat; i++){ ncols_send[i] = xadj[i+1]-xadj[i]; } ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); ierr = PetscSFSetGraph(sf,nroots,nleaves,PETSC_NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr); ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); ierr = PetscSFBcastBegin(sf,MPIU_INT,ncols_send,ncols_recv);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sf,MPIU_INT,ncols_send,ncols_recv);CHKERRQ(ierr); ierr = PetscSFBcastBegin(sf,MPIU_INT,xadj,xadj_recv);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sf,MPIU_INT,xadj,xadj_recv);CHKERRQ(ierr); ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); Ncols_recv =0; for(i=0; i<nlrows_is; i++){ Ncols_recv += ncols_recv[i]; ncols_recv_offsets[i+1] = ncols_recv[i]+ncols_recv_offsets[i]; } Ncols_send = 0; for(i=0; i<nlrows_mat; i++){ Ncols_send += ncols_send[i]; } ierr = PetscCalloc1(Ncols_recv,&iremote);CHKERRQ(ierr); ierr = PetscCalloc1(Ncols_recv,&adjncy_recv);CHKERRQ(ierr); nleaves = Ncols_recv; Ncols_recv = 0; for(i=0; i<nlrows_is; i++){ ierr = PetscLayoutFindOwner(rmap,irows_indices[i],&owner);CHKERRQ(ierr); for(j=0; j<ncols_recv[i]; j++){ iremote[Ncols_recv].rank = owner; iremote[Ncols_recv++].index = xadj_recv[i]+j; } } ierr = ISRestoreIndices(irows,&irows_indices);CHKERRQ(ierr); /*if we need to deal with edge weights ???*/ if(a->values){isvalue=1;}else{isvalue=0;} /*involve a global communication */ /*ierr = MPI_Allreduce(&isvalue,&isvalue,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr);*/ if(isvalue){ierr = PetscCalloc1(Ncols_recv,&values_recv);CHKERRQ(ierr);} nroots = Ncols_send; ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); ierr = PetscSFSetGraph(sf,nroots,nleaves,PETSC_NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr); ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); ierr = PetscSFBcastBegin(sf,MPIU_INT,adjncy,adjncy_recv);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sf,MPIU_INT,adjncy,adjncy_recv);CHKERRQ(ierr); if(isvalue){ ierr = PetscSFBcastBegin(sf,MPIU_INT,a->values,values_recv);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sf,MPIU_INT,a->values,values_recv);CHKERRQ(ierr); } ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); ierr = MatRestoreRowIJ(adj,0,PETSC_FALSE,PETSC_FALSE,&nlrows_mat,&xadj,&adjncy,&done);CHKERRQ(ierr); ierr = ISGetLocalSize(icols,&icols_n);CHKERRQ(ierr); ierr = ISGetIndices(icols,&icols_indices);CHKERRQ(ierr); rnclos = 0; for(i=0; i<nlrows_is; i++){ for(j=ncols_recv_offsets[i]; j<ncols_recv_offsets[i+1]; j++){ ierr = PetscFindInt(adjncy_recv[j], icols_n, icols_indices, &loc);CHKERRQ(ierr); if(loc<0){ adjncy_recv[j] = -1; if(isvalue) values_recv[j] = -1; ncols_recv[i]--; }else{ rnclos++; } } } ierr = ISRestoreIndices(icols,&icols_indices);CHKERRQ(ierr); ierr = PetscCalloc1(rnclos,&sadjncy);CHKERRQ(ierr); if(isvalue) {ierr = PetscCalloc1(rnclos,&svalues);CHKERRQ(ierr);} ierr = PetscCalloc1(nlrows_is+1,&sxadj);CHKERRQ(ierr); rnclos = 0; for(i=0; i<nlrows_is; i++){ for(j=ncols_recv_offsets[i]; j<ncols_recv_offsets[i+1]; j++){ if(adjncy_recv[j]<0) continue; sadjncy[rnclos] = adjncy_recv[j]; if(isvalue) svalues[rnclos] = values_recv[j]; rnclos++; } } for(i=0; i<nlrows_is; i++){ sxadj[i+1] = sxadj[i]+ncols_recv[i]; } if(sadj_xadj) { *sadj_xadj = sxadj;}else { ierr = PetscFree(sxadj);CHKERRQ(ierr);} if(sadj_adjncy){ *sadj_adjncy = sadjncy;}else{ ierr = PetscFree(sadjncy);CHKERRQ(ierr);} if(sadj_values){ if(isvalue) *sadj_values = svalues; else *sadj_values=0; }else{ if(isvalue) {ierr = PetscFree(svalues);CHKERRQ(ierr);} } ierr = PetscFree4(ncols_send,xadj_recv,ncols_recv_offsets,ncols_recv);CHKERRQ(ierr); ierr = PetscFree(adjncy_recv);CHKERRQ(ierr); if(isvalue) {ierr = PetscFree(values_recv);CHKERRQ(ierr);} PetscFunctionReturn(0); }
static PetscErrorCode MatGetSubMatrices_MPIAdj_Private(Mat mat,PetscInt n,const IS irow[],const IS icol[],PetscBool subcomm,MatReuse scall,Mat *submat[]) { PetscInt i,irow_n,icol_n,*sxadj,*sadjncy,*svalues; PetscInt *indices,nindx,j,k,loc; PetscMPIInt issame; const PetscInt *irow_indices,*icol_indices; MPI_Comm scomm_row,scomm_col,scomm_mat; PetscErrorCode ierr; PetscFunctionBegin; nindx = 0; /* * Estimate a maximum number for allocating memory */ for(i=0; i<n; i++){ ierr = ISGetLocalSize(irow[i],&irow_n);CHKERRQ(ierr); ierr = ISGetLocalSize(icol[i],&icol_n);CHKERRQ(ierr); nindx = nindx>(irow_n+icol_n)? nindx:(irow_n+icol_n); } ierr = PetscCalloc1(nindx,&indices);CHKERRQ(ierr); /* construct a submat */ for(i=0; i<n; i++){ /*comms */ if(subcomm){ ierr = PetscObjectGetComm((PetscObject)irow[i],&scomm_row);CHKERRQ(ierr); ierr = PetscObjectGetComm((PetscObject)icol[i],&scomm_col);CHKERRQ(ierr); ierr = MPI_Comm_compare(scomm_row,scomm_col,&issame);CHKERRQ(ierr); if(issame != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"row index set must have the same comm as the col index set\n"); ierr = MPI_Comm_compare(scomm_row,PETSC_COMM_SELF,&issame);CHKERRQ(ierr); if(issame == MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP," can not use PETSC_COMM_SELF as comm when extracting a parallel submatrix\n"); }else{ scomm_row = PETSC_COMM_SELF; } /*get sub-matrix data*/ sxadj=0; sadjncy=0; svalues=0; ierr = MatGetSubMatrix_MPIAdj_data(mat,irow[i],icol[i],&sxadj,&sadjncy,&svalues);CHKERRQ(ierr); ierr = ISGetLocalSize(irow[i],&irow_n);CHKERRQ(ierr); ierr = ISGetLocalSize(icol[i],&icol_n);CHKERRQ(ierr); ierr = ISGetIndices(irow[i],&irow_indices);CHKERRQ(ierr); ierr = PetscMemcpy(indices,irow_indices,sizeof(PetscInt)*irow_n);CHKERRQ(ierr); ierr = ISRestoreIndices(irow[i],&irow_indices);CHKERRQ(ierr); ierr = ISGetIndices(icol[i],&icol_indices);CHKERRQ(ierr); ierr = PetscMemcpy(indices+irow_n,icol_indices,sizeof(PetscInt)*icol_n);CHKERRQ(ierr); ierr = ISRestoreIndices(icol[i],&icol_indices);CHKERRQ(ierr); nindx = irow_n+icol_n; ierr = PetscSortRemoveDupsInt(&nindx,indices);CHKERRQ(ierr); /* renumber columns */ for(j=0; j<irow_n; j++){ for(k=sxadj[j]; k<sxadj[j+1]; k++){ ierr = PetscFindInt(sadjncy[k],nindx,indices,&loc);CHKERRQ(ierr); #if PETSC_USE_DEBUG if(loc<0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"can not find col %d \n",sadjncy[k]); #endif sadjncy[k] = loc; } } if(scall==MAT_INITIAL_MATRIX){ ierr = MatCreateMPIAdj(scomm_row,irow_n,icol_n,sxadj,sadjncy,svalues,submat[i]);CHKERRQ(ierr); }else{ Mat sadj = *(submat[i]); Mat_MPIAdj *sa = (Mat_MPIAdj*)((sadj)->data); ierr = PetscObjectGetComm((PetscObject)sadj,&scomm_mat);CHKERRQ(ierr); ierr = MPI_Comm_compare(scomm_row,scomm_mat,&issame);CHKERRQ(ierr); if(issame != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"submatrix must have the same comm as the col index set\n"); ierr = PetscMemcpy(sa->i,sxadj,sizeof(PetscInt)*(irow_n+1));CHKERRQ(ierr); ierr = PetscMemcpy(sa->j,sadjncy,sizeof(PetscInt)*sxadj[irow_n]);CHKERRQ(ierr); if(svalues){ierr = PetscMemcpy(sa->values,svalues,sizeof(PetscInt)*sxadj[irow_n]);CHKERRQ(ierr);} ierr = PetscFree(sxadj);CHKERRQ(ierr); ierr = PetscFree(sadjncy);CHKERRQ(ierr); if(svalues) {ierr = PetscFree(svalues);CHKERRQ(ierr);} } } ierr = PetscFree(indices);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode PCBDDCGraphSetUp(PCBDDCGraph graph, PetscInt custom_minimal_size, IS neumann_is, IS dirichlet_is, PetscInt n_ISForDofs, IS ISForDofs[], IS custom_primal_vertices) { IS subset,subset_n; MPI_Comm comm; const PetscInt *is_indices; PetscInt n_neigh,*neigh,*n_shared,**shared,*queue_global; PetscInt i,j,k,s,total_counts,nodes_touched,is_size; PetscMPIInt commsize; PetscBool same_set,mirrors_found; PetscErrorCode ierr; PetscFunctionBegin; PetscValidLogicalCollectiveInt(graph->l2gmap,custom_minimal_size,2); if (neumann_is) { PetscValidHeaderSpecific(neumann_is,IS_CLASSID,3); PetscCheckSameComm(graph->l2gmap,1,neumann_is,3); } graph->has_dirichlet = PETSC_FALSE; if (dirichlet_is) { PetscValidHeaderSpecific(dirichlet_is,IS_CLASSID,4); PetscCheckSameComm(graph->l2gmap,1,dirichlet_is,4); graph->has_dirichlet = PETSC_TRUE; } PetscValidLogicalCollectiveInt(graph->l2gmap,n_ISForDofs,5); for (i=0;i<n_ISForDofs;i++) { PetscValidHeaderSpecific(ISForDofs[i],IS_CLASSID,6); PetscCheckSameComm(graph->l2gmap,1,ISForDofs[i],6); } if (custom_primal_vertices) { PetscValidHeaderSpecific(custom_primal_vertices,IS_CLASSID,6); PetscCheckSameComm(graph->l2gmap,1,custom_primal_vertices,7); } ierr = PetscObjectGetComm((PetscObject)(graph->l2gmap),&comm);CHKERRQ(ierr); ierr = MPI_Comm_size(comm,&commsize);CHKERRQ(ierr); /* custom_minimal_size */ graph->custom_minimal_size = custom_minimal_size; /* get info l2gmap and allocate work vectors */ ierr = ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); /* check if we have any local periodic nodes (periodic BCs) */ mirrors_found = PETSC_FALSE; if (graph->nvtxs && n_neigh) { for (i=0; i<n_shared[0]; i++) graph->count[shared[0][i]] += 1; for (i=0; i<n_shared[0]; i++) { if (graph->count[shared[0][i]] > 1) { mirrors_found = PETSC_TRUE; break; } } } /* compute local mirrors (if any) */ if (mirrors_found) { IS to,from; PetscInt *local_indices,*global_indices; ierr = ISCreateStride(PETSC_COMM_SELF,graph->nvtxs,0,1,&to);CHKERRQ(ierr); ierr = ISLocalToGlobalMappingApplyIS(graph->l2gmap,to,&from);CHKERRQ(ierr); /* get arrays of local and global indices */ ierr = PetscMalloc1(graph->nvtxs,&local_indices);CHKERRQ(ierr); ierr = ISGetIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); ierr = PetscMemcpy(local_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); ierr = ISRestoreIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); ierr = PetscMalloc1(graph->nvtxs,&global_indices);CHKERRQ(ierr); ierr = ISGetIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); ierr = PetscMemcpy(global_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); ierr = ISRestoreIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); /* allocate space for mirrors */ ierr = PetscMalloc2(graph->nvtxs,&graph->mirrors,graph->nvtxs,&graph->mirrors_set);CHKERRQ(ierr); ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); graph->mirrors_set[0] = 0; k=0; for (i=0;i<n_shared[0];i++) { j=shared[0][i]; if (graph->count[j] > 1) { graph->mirrors[j]++; k++; } } /* allocate space for set of mirrors */ ierr = PetscMalloc1(k,&graph->mirrors_set[0]);CHKERRQ(ierr); for (i=1;i<graph->nvtxs;i++) graph->mirrors_set[i]=graph->mirrors_set[i-1]+graph->mirrors[i-1]; /* fill arrays */ ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); for (j=0;j<n_shared[0];j++) { i=shared[0][j]; if (graph->count[i] > 1) graph->mirrors_set[i][graph->mirrors[i]++]=global_indices[i]; } ierr = PetscSortIntWithArray(graph->nvtxs,global_indices,local_indices);CHKERRQ(ierr); for (i=0;i<graph->nvtxs;i++) { if (graph->mirrors[i] > 0) { ierr = PetscFindInt(graph->mirrors_set[i][0],graph->nvtxs,global_indices,&k);CHKERRQ(ierr); j = global_indices[k]; while ( k > 0 && global_indices[k-1] == j) k--; for (j=0;j<graph->mirrors[i];j++) { graph->mirrors_set[i][j]=local_indices[k+j]; } ierr = PetscSortInt(graph->mirrors[i],graph->mirrors_set[i]);CHKERRQ(ierr); } } ierr = PetscFree(local_indices);CHKERRQ(ierr); ierr = PetscFree(global_indices);CHKERRQ(ierr); ierr = ISDestroy(&to);CHKERRQ(ierr); ierr = ISDestroy(&from);CHKERRQ(ierr); } ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); /* Count total number of neigh per node */ k = 0; for (i=1;i<n_neigh;i++) { k += n_shared[i]; for (j=0;j<n_shared[i];j++) { graph->count[shared[i][j]] += 1; } } /* Allocate space for storing the set of neighbours for each node */ if (graph->nvtxs) { ierr = PetscMalloc1(k,&graph->neighbours_set[0]);CHKERRQ(ierr); } for (i=1;i<graph->nvtxs;i++) { /* dont count myself */ graph->neighbours_set[i]=graph->neighbours_set[i-1]+graph->count[i-1]; } /* Get information for sharing subdomains */ ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); for (i=1;i<n_neigh;i++) { /* dont count myself */ s = n_shared[i]; for (j=0;j<s;j++) { k = shared[i][j]; graph->neighbours_set[k][graph->count[k]] = neigh[i]; graph->count[k] += 1; } } /* sort set of sharing subdomains */ for (i=0;i<graph->nvtxs;i++) { ierr = PetscSortRemoveDupsInt(&graph->count[i],graph->neighbours_set[i]);CHKERRQ(ierr); } /* free memory allocated by ISLocalToGlobalMappingGetInfo */ ierr = ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); /* Get info for dofs splitting User can specify just a subset; an additional field is considered as a complementary field */ for (i=0;i<graph->nvtxs;i++) graph->which_dof[i] = n_ISForDofs; /* by default a dof belongs to the complement set */ for (i=0;i<n_ISForDofs;i++) { ierr = ISGetLocalSize(ISForDofs[i],&is_size);CHKERRQ(ierr); ierr = ISGetIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); for (j=0;j<is_size;j++) { if (is_indices[j] > -1 && is_indices[j] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ graph->which_dof[is_indices[j]] = i; } } ierr = ISRestoreIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); } /* Take into account Neumann nodes */ if (neumann_is) { ierr = ISGetLocalSize(neumann_is,&is_size);CHKERRQ(ierr); ierr = ISGetIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); for (i=0;i<is_size;i++) { if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ graph->special_dof[is_indices[i]] = PCBDDCGRAPH_NEUMANN_MARK; } } ierr = ISRestoreIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); } /* Take into account Dirichlet nodes (they overwrite any neumann boundary mark previously set) */ if (dirichlet_is) { ierr = ISGetLocalSize(dirichlet_is,&is_size);CHKERRQ(ierr); ierr = ISGetIndices(dirichlet_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); for (i=0;i<is_size;i++){ if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ if (commsize > graph->commsizelimit) { /* dirichlet nodes treated as internal */ ierr = PetscBTSet(graph->touched,is_indices[i]);CHKERRQ(ierr); graph->subset[is_indices[i]] = 0; } graph->special_dof[is_indices[i]] = PCBDDCGRAPH_DIRICHLET_MARK; } } ierr = ISRestoreIndices(dirichlet_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); } /* mark local periodic nodes (if any) and adapt CSR graph (if any) */ if (graph->mirrors) { for (i=0;i<graph->nvtxs;i++) if (graph->mirrors[i]) graph->special_dof[i] = PCBDDCGRAPH_LOCAL_PERIODIC_MARK; if (graph->xadj) { PetscInt *new_xadj,*new_adjncy; /* sort CSR graph */ for (i=0;i<graph->nvtxs;i++) ierr = PetscSortInt(graph->xadj[i+1]-graph->xadj[i],&graph->adjncy[graph->xadj[i]]);CHKERRQ(ierr); /* adapt local CSR graph in case of local periodicity */ k = 0; for (i=0;i<graph->nvtxs;i++) for (j=graph->xadj[i];j<graph->xadj[i+1];j++) k += graph->mirrors[graph->adjncy[j]]; ierr = PetscMalloc1(graph->nvtxs+1,&new_xadj);CHKERRQ(ierr); ierr = PetscMalloc1(k+graph->xadj[graph->nvtxs],&new_adjncy);CHKERRQ(ierr); new_xadj[0] = 0; for (i=0;i<graph->nvtxs;i++) { k = graph->xadj[i+1]-graph->xadj[i]; ierr = PetscMemcpy(&new_adjncy[new_xadj[i]],&graph->adjncy[graph->xadj[i]],k*sizeof(PetscInt));CHKERRQ(ierr); new_xadj[i+1] = new_xadj[i]+k; for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { k = graph->mirrors[graph->adjncy[j]]; ierr = PetscMemcpy(&new_adjncy[new_xadj[i+1]],graph->mirrors_set[graph->adjncy[j]],k*sizeof(PetscInt));CHKERRQ(ierr); new_xadj[i+1] += k; } k = new_xadj[i+1]-new_xadj[i]; ierr = PetscSortRemoveDupsInt(&k,&new_adjncy[new_xadj[i]]);CHKERRQ(ierr); new_xadj[i+1] = new_xadj[i]+k; } /* set new CSR into graph */ ierr = PetscFree(graph->xadj);CHKERRQ(ierr); ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); graph->xadj = new_xadj; graph->adjncy = new_adjncy; } } /* mark special nodes (if any) -> each will become a single node equivalence class */ if (custom_primal_vertices) { ierr = ISGetLocalSize(custom_primal_vertices,&is_size);CHKERRQ(ierr); ierr = ISGetIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); for (i=0,j=0;i<is_size;i++){ if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs && graph->special_dof[is_indices[i]] != PCBDDCGRAPH_DIRICHLET_MARK) { /* out of bounds indices (if any) are skipped */ graph->special_dof[is_indices[i]] = PCBDDCGRAPH_SPECIAL_MARK-j; j++; } } ierr = ISRestoreIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); } /* mark interior nodes (if commsize > graph->commsizelimit) as touched and belonging to partition number 0 */ if (commsize > graph->commsizelimit) { for (i=0;i<graph->nvtxs;i++) { if (!graph->count[i]) { ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); graph->subset[i] = 0; } } } /* init graph structure and compute default subsets */ nodes_touched = 0; for (i=0;i<graph->nvtxs;i++) { if (PetscBTLookup(graph->touched,i)) { nodes_touched++; } } i = 0; graph->ncc = 0; total_counts = 0; /* allocated space for queues */ if (commsize == graph->commsizelimit) { ierr = PetscMalloc2(graph->nvtxs+1,&graph->cptr,graph->nvtxs,&graph->queue);CHKERRQ(ierr); } else { PetscInt nused = graph->nvtxs - nodes_touched; ierr = PetscMalloc2(nused+1,&graph->cptr,nused,&graph->queue);CHKERRQ(ierr); } while (nodes_touched<graph->nvtxs) { /* find first untouched node in local ordering */ while (PetscBTLookup(graph->touched,i)) i++; ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); graph->subset[i] = graph->ncc+1; graph->cptr[graph->ncc] = total_counts; graph->queue[total_counts] = i; total_counts++; nodes_touched++; /* now find all other nodes having the same set of sharing subdomains */ for (j=i+1;j<graph->nvtxs;j++) { /* check for same number of sharing subdomains, dof number and same special mark */ if (!PetscBTLookup(graph->touched,j) && graph->count[i] == graph->count[j] && graph->which_dof[i] == graph->which_dof[j] && graph->special_dof[i] == graph->special_dof[j]) { /* check for same set of sharing subdomains */ same_set = PETSC_TRUE; for (k=0;k<graph->count[j];k++){ if (graph->neighbours_set[i][k] != graph->neighbours_set[j][k]) { same_set = PETSC_FALSE; } } /* I found a friend of mine */ if (same_set) { ierr = PetscBTSet(graph->touched,j);CHKERRQ(ierr); graph->subset[j] = graph->ncc+1; nodes_touched++; graph->queue[total_counts] = j; total_counts++; } } } graph->ncc++; } /* set default number of subsets (at this point no info on csr and/or local_subs has been taken into account, so n_subsets = ncc */ graph->n_subsets = graph->ncc; ierr = PetscMalloc1(graph->n_subsets,&graph->subset_ncc);CHKERRQ(ierr); for (i=0;i<graph->n_subsets;i++) { graph->subset_ncc[i] = 1; } /* final pointer */ graph->cptr[graph->ncc] = total_counts; /* For consistency reasons (among neighbours), I need to sort (by global ordering) each connected component */ /* Get a reference node (min index in global ordering) for each subset for tagging messages */ ierr = PetscMalloc1(graph->ncc,&graph->subset_ref_node);CHKERRQ(ierr); ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_global);CHKERRQ(ierr); ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);CHKERRQ(ierr); for (j=0;j<graph->ncc;j++) { ierr = PetscSortIntWithArray(graph->cptr[j+1]-graph->cptr[j],&queue_global[graph->cptr[j]],&graph->queue[graph->cptr[j]]);CHKERRQ(ierr); graph->subset_ref_node[j] = graph->queue[graph->cptr[j]]; } ierr = PetscFree(queue_global);CHKERRQ(ierr); graph->queue_sorted = PETSC_TRUE; /* save information on subsets (needed when analyzing the connected components) */ if (graph->ncc) { ierr = PetscMalloc2(graph->ncc,&graph->subset_size,graph->ncc,&graph->subset_idxs);CHKERRQ(ierr); ierr = PetscMalloc1(graph->cptr[graph->ncc],&graph->subset_idxs[0]);CHKERRQ(ierr); ierr = PetscMemzero(graph->subset_idxs[0],graph->cptr[graph->ncc]*sizeof(PetscInt));CHKERRQ(ierr); for (j=1;j<graph->ncc;j++) { graph->subset_size[j-1] = graph->cptr[j] - graph->cptr[j-1]; graph->subset_idxs[j] = graph->subset_idxs[j-1] + graph->subset_size[j-1]; } graph->subset_size[graph->ncc-1] = graph->cptr[graph->ncc] - graph->cptr[graph->ncc-1]; ierr = PetscMemcpy(graph->subset_idxs[0],graph->queue,graph->cptr[graph->ncc]*sizeof(PetscInt));CHKERRQ(ierr); } /* renumber reference nodes */ ierr = ISCreateGeneral(PetscObjectComm((PetscObject)(graph->l2gmap)),graph->ncc,graph->subset_ref_node,PETSC_COPY_VALUES,&subset_n);CHKERRQ(ierr); ierr = ISLocalToGlobalMappingApplyIS(graph->l2gmap,subset_n,&subset);CHKERRQ(ierr); ierr = ISDestroy(&subset_n);CHKERRQ(ierr); ierr = ISRenumber(subset,NULL,NULL,&subset_n);CHKERRQ(ierr); ierr = ISDestroy(&subset);CHKERRQ(ierr); ierr = ISGetLocalSize(subset_n,&k);CHKERRQ(ierr); if (k != graph->ncc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Invalid size of new subset! %D != %D",k,graph->ncc); ierr = ISGetIndices(subset_n,&is_indices);CHKERRQ(ierr); ierr = PetscMemcpy(graph->subset_ref_node,is_indices,graph->ncc*sizeof(PetscInt));CHKERRQ(ierr); ierr = ISRestoreIndices(subset_n,&is_indices);CHKERRQ(ierr); ierr = ISDestroy(&subset_n);CHKERRQ(ierr); /* free workspace */ graph->setupcalled = PETSC_TRUE; PetscFunctionReturn(0); }
PetscErrorCode DMLabelSetValue(DMLabel label, PetscInt point, PetscInt value) { PetscInt v, loc; PetscErrorCode ierr; PetscFunctionBegin; /* Find, or add, label value */ for (v = 0; v < label->numStrata; ++v) { if (label->stratumValues[v] == value) break; } if (v >= label->numStrata) { PetscInt *tmpV, *tmpO, *tmpS; ierr = PetscMalloc3(label->numStrata+1,PetscInt,&tmpV,label->numStrata+2,PetscInt,&tmpO,label->numStrata+1,PetscInt,&tmpS);CHKERRQ(ierr); for (v = 0; v < label->numStrata; ++v) { tmpV[v] = label->stratumValues[v]; tmpO[v] = label->stratumOffsets[v]; tmpS[v] = label->stratumSizes[v]; } tmpV[v] = value; tmpO[v] = v == 0 ? 0 : label->stratumOffsets[v]; tmpS[v] = 0; tmpO[v+1] = tmpO[v]; ++label->numStrata; ierr = PetscFree3(label->stratumValues,label->stratumOffsets,label->stratumSizes);CHKERRQ(ierr); label->stratumValues = tmpV; label->stratumOffsets = tmpO; label->stratumSizes = tmpS; } /* Check whether point exists */ ierr = PetscFindInt(point,label->stratumSizes[v],label->points+label->stratumOffsets[v],&loc);CHKERRQ(ierr); if (loc < 0) { PetscInt off = label->stratumOffsets[v] - (loc+1); /* decode insert location */ /* Check for reallocation */ if (label->stratumSizes[v] >= label->stratumOffsets[v+1]-label->stratumOffsets[v]) { PetscInt oldSize = label->stratumOffsets[v+1]-label->stratumOffsets[v]; PetscInt newSize = PetscMax(10, 2*oldSize); /* Double the size, since 2 is the optimal base for this online algorithm */ PetscInt shift = newSize - oldSize; PetscInt allocSize = label->stratumOffsets[label->numStrata] + shift; PetscInt *newPoints; PetscInt w, q; ierr = PetscMalloc(allocSize * sizeof(PetscInt), &newPoints);CHKERRQ(ierr); for (q = 0; q < label->stratumOffsets[v]+label->stratumSizes[v]; ++q) { newPoints[q] = label->points[q]; } for (w = v+1; w < label->numStrata; ++w) { for (q = label->stratumOffsets[w]; q < label->stratumOffsets[w]+label->stratumSizes[w]; ++q) { newPoints[q+shift] = label->points[q]; } label->stratumOffsets[w] += shift; } label->stratumOffsets[label->numStrata] += shift; ierr = PetscFree(label->points);CHKERRQ(ierr); label->points = newPoints; } ierr = PetscMemmove(&label->points[off+1], &label->points[off], (label->stratumSizes[v]+(loc+1)) * sizeof(PetscInt));CHKERRQ(ierr); label->points[off] = point; ++label->stratumSizes[v]; } PetscFunctionReturn(0); }