PetscErrorCode MatPartitioningHierarchical_ReassembleFineparts(Mat adj, IS fineparts, ISLocalToGlobalMapping mapping, IS *sfineparts) { PetscInt *local_indices, *global_indices,*owners,*sfineparts_indices,localsize,i; const PetscInt *ranges,*fineparts_indices; PetscMPIInt rank; MPI_Comm comm; PetscLayout rmap; PetscSFNode *remote; PetscSF sf; PetscErrorCode ierr; PetscFunctionBegin; /*get communicator */ ierr = PetscObjectGetComm((PetscObject)adj,&comm);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); ierr = MatGetLayouts(adj,&rmap,PETSC_NULL);CHKERRQ(ierr); ierr = ISGetLocalSize(fineparts,&localsize);CHKERRQ(ierr); ierr = PetscCalloc2(localsize,&global_indices,localsize,&local_indices);CHKERRQ(ierr); for(i=0; i<localsize; i++){ local_indices[i] = i; } /*global indices */ ierr = ISLocalToGlobalMappingApply(mapping,localsize,local_indices,global_indices);CHKERRQ(ierr); ierr = PetscCalloc1(localsize,&owners);CHKERRQ(ierr); /*find owners for global indices */ for(i=0; i<localsize; i++){ ierr = PetscLayoutFindOwner(rmap,global_indices[i],&owners[i]);CHKERRQ(ierr); } /*ranges */ ierr = PetscLayoutGetRanges(rmap,&ranges);CHKERRQ(ierr); ierr = PetscCalloc1(ranges[rank+1]-ranges[rank],&sfineparts_indices);CHKERRQ(ierr); ierr = ISGetIndices(fineparts,&fineparts_indices);CHKERRQ(ierr); /*create a SF to exchange data */ ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); ierr = PetscCalloc1(localsize,&remote);CHKERRQ(ierr); for(i=0; i<localsize; i++){ remote[i].rank = owners[i]; remote[i].index = global_indices[i]-ranges[owners[i]]; } ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr); /*not sure how to add prefix to sf*/ ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); ierr = PetscSFSetGraph(sf,localsize,localsize,PETSC_NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);CHKERRQ(ierr); ierr = PetscSFReduceBegin(sf,MPIU_INT,fineparts_indices,sfineparts_indices,MPIU_REPLACE);CHKERRQ(ierr); ierr = PetscSFReduceEnd(sf,MPIU_INT,fineparts_indices,sfineparts_indices,MPIU_REPLACE);CHKERRQ(ierr); ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); ierr = ISRestoreIndices(fineparts,&fineparts_indices);CHKERRQ(ierr); /* comm self */ ierr = ISCreateGeneral(comm,ranges[rank+1]-ranges[rank],sfineparts_indices,PETSC_OWN_POINTER,sfineparts);CHKERRQ(ierr); ierr = PetscFree2(global_indices,local_indices);CHKERRQ(ierr); ierr = PetscFree(owners);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode DMInterpolationSetUp(DMInterpolationInfo ctx, DM dm, PetscBool redundantPoints) { MPI_Comm comm = ctx->comm; PetscScalar *a; PetscInt p, q, i; PetscMPIInt rank, size; PetscErrorCode ierr; Vec pointVec; IS cellIS; PetscLayout layout; PetscReal *globalPoints; PetscScalar *globalPointsScalar; const PetscInt *ranges; PetscMPIInt *counts, *displs; const PetscInt *foundCells; PetscMPIInt *foundProcs, *globalProcs; PetscInt n, N; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); if (ctx->dim < 0) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); /* Locate points */ n = ctx->nInput; if (!redundantPoints) { ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr); ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); ierr = PetscLayoutSetLocalSize(layout, n);CHKERRQ(ierr); ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr); ierr = PetscLayoutGetSize(layout, &N);CHKERRQ(ierr); /* Communicate all points to all processes */ ierr = PetscMalloc3(N*ctx->dim,&globalPoints,size,&counts,size,&displs);CHKERRQ(ierr); ierr = PetscLayoutGetRanges(layout, &ranges);CHKERRQ(ierr); for (p = 0; p < size; ++p) { counts[p] = (ranges[p+1] - ranges[p])*ctx->dim; displs[p] = ranges[p]*ctx->dim; } ierr = MPI_Allgatherv(ctx->points, n*ctx->dim, MPIU_REAL, globalPoints, counts, displs, MPIU_REAL, comm);CHKERRQ(ierr); } else { N = n; globalPoints = ctx->points; counts = displs = NULL; layout = NULL; } #if 0 ierr = PetscMalloc3(N,&foundCells,N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); /* foundCells[p] = m->locatePoint(&globalPoints[p*ctx->dim]); */ #else #if defined(PETSC_USE_COMPLEX) ierr = PetscMalloc1(N,&globalPointsScalar);CHKERRQ(ierr); for (i=0; i<N; i++) globalPointsScalar[i] = globalPoints[i]; #else globalPointsScalar = globalPoints; #endif ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, ctx->dim, N*ctx->dim, globalPointsScalar, &pointVec);CHKERRQ(ierr); ierr = PetscMalloc2(N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); ierr = DMLocatePoints(dm, pointVec, &cellIS);CHKERRQ(ierr); ierr = ISGetIndices(cellIS, &foundCells);CHKERRQ(ierr); #endif for (p = 0; p < N; ++p) { if (foundCells[p] >= 0) foundProcs[p] = rank; else foundProcs[p] = size; } /* Let the lowest rank process own each point */ ierr = MPI_Allreduce(foundProcs, globalProcs, N, MPI_INT, MPI_MIN, comm);CHKERRQ(ierr); ctx->n = 0; for (p = 0; p < N; ++p) { if (globalProcs[p] == size) SETERRQ4(comm, PETSC_ERR_PLIB, "Point %d: %g %g %g not located in mesh", p, globalPoints[p*ctx->dim+0], ctx->dim > 1 ? globalPoints[p*ctx->dim+1] : 0.0, ctx->dim > 2 ? globalPoints[p*ctx->dim+2] : 0.0); else if (globalProcs[p] == rank) ctx->n++; } /* Create coordinates vector and array of owned cells */ ierr = PetscMalloc1(ctx->n, &ctx->cells);CHKERRQ(ierr); ierr = VecCreate(comm, &ctx->coords);CHKERRQ(ierr); ierr = VecSetSizes(ctx->coords, ctx->n*ctx->dim, PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetBlockSize(ctx->coords, ctx->dim);CHKERRQ(ierr); ierr = VecSetType(ctx->coords,VECSTANDARD);CHKERRQ(ierr); ierr = VecGetArray(ctx->coords, &a);CHKERRQ(ierr); for (p = 0, q = 0, i = 0; p < N; ++p) { if (globalProcs[p] == rank) { PetscInt d; for (d = 0; d < ctx->dim; ++d, ++i) a[i] = globalPoints[p*ctx->dim+d]; ctx->cells[q++] = foundCells[p]; } } ierr = VecRestoreArray(ctx->coords, &a);CHKERRQ(ierr); #if 0 ierr = PetscFree3(foundCells,foundProcs,globalProcs);CHKERRQ(ierr); #else ierr = PetscFree2(foundProcs,globalProcs);CHKERRQ(ierr); ierr = ISRestoreIndices(cellIS, &foundCells);CHKERRQ(ierr); ierr = ISDestroy(&cellIS);CHKERRQ(ierr); ierr = VecDestroy(&pointVec);CHKERRQ(ierr); #endif if ((void*)globalPointsScalar != (void*)globalPoints) {ierr = PetscFree(globalPointsScalar);CHKERRQ(ierr);} if (!redundantPoints) {ierr = PetscFree3(globalPoints,counts,displs);CHKERRQ(ierr);} ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); PetscFunctionReturn(0); }