PetscErrorCode TestMatZeroRows(Mat A, Mat Afull, PetscBool squaretest, IS is, PetscScalar diag) { Mat B,Bcheck,B2 = NULL,lB; Vec x = NULL, b = NULL, b2 = NULL; ISLocalToGlobalMapping l2gr,l2gc; PetscReal error; char diagstr[16]; const PetscInt *idxs; PetscInt rst,ren,i,n,N,d; PetscMPIInt rank; PetscBool miss,haszerorows; PetscErrorCode ierr; PetscFunctionBeginUser; if (diag == 0.) { ierr = PetscStrcpy(diagstr,"zero");CHKERRQ(ierr); } else { ierr = PetscStrcpy(diagstr,"nonzero");CHKERRQ(ierr); } ierr = ISView(is,NULL);CHKERRQ(ierr); ierr = MatGetLocalToGlobalMapping(A,&l2gr,&l2gc);CHKERRQ(ierr); /* tests MatDuplicate and MatCopy */ if (diag == 0.) { ierr = MatDuplicate(A,MAT_COPY_VALUES,&B);CHKERRQ(ierr); } else { ierr = MatDuplicate(A,MAT_DO_NOT_COPY_VALUES,&B);CHKERRQ(ierr); ierr = MatCopy(A,B,SAME_NONZERO_PATTERN);CHKERRQ(ierr); } ierr = MatISGetLocalMat(B,&lB);CHKERRQ(ierr); ierr = MatHasOperation(lB,MATOP_ZERO_ROWS,&haszerorows);CHKERRQ(ierr); if (squaretest && haszerorows) { ierr = MatCreateVecs(B,&x,&b);CHKERRQ(ierr); ierr = MatDuplicate(B,MAT_COPY_VALUES,&B2);CHKERRQ(ierr); ierr = VecSetLocalToGlobalMapping(b,l2gr);CHKERRQ(ierr); ierr = VecSetLocalToGlobalMapping(x,l2gc);CHKERRQ(ierr); ierr = VecSetRandom(x,NULL);CHKERRQ(ierr); ierr = VecSetRandom(b,NULL);CHKERRQ(ierr); /* mimic b[is] = x[is] */ ierr = VecDuplicate(b,&b2);CHKERRQ(ierr); ierr = VecSetLocalToGlobalMapping(b2,l2gr);CHKERRQ(ierr); ierr = VecCopy(b,b2);CHKERRQ(ierr); ierr = ISGetLocalSize(is,&n);CHKERRQ(ierr); ierr = ISGetIndices(is,&idxs);CHKERRQ(ierr); ierr = VecGetSize(x,&N);CHKERRQ(ierr); for (i=0;i<n;i++) { if (0 <= idxs[i] && idxs[i] < N) { ierr = VecSetValue(b2,idxs[i],diag,INSERT_VALUES);CHKERRQ(ierr); ierr = VecSetValue(x,idxs[i],1.,INSERT_VALUES);CHKERRQ(ierr); } } ierr = VecAssemblyBegin(b2);CHKERRQ(ierr); ierr = VecAssemblyEnd(b2);CHKERRQ(ierr); ierr = VecAssemblyBegin(x);CHKERRQ(ierr); ierr = VecAssemblyEnd(x);CHKERRQ(ierr); ierr = ISRestoreIndices(is,&idxs);CHKERRQ(ierr); /* test ZeroRows on MATIS */ ierr = PetscPrintf(PETSC_COMM_WORLD,"Test MatZeroRows (diag %s)\n",diagstr);CHKERRQ(ierr); ierr = MatZeroRowsIS(B,is,diag,x,b);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Test MatZeroRowsColumns (diag %s)\n",diagstr);CHKERRQ(ierr); ierr = MatZeroRowsColumnsIS(B2,is,diag,NULL,NULL);CHKERRQ(ierr); } else if (haszerorows) { /* test ZeroRows on MATIS */ ierr = PetscPrintf(PETSC_COMM_WORLD,"Test MatZeroRows (diag %s)\n",diagstr);CHKERRQ(ierr); ierr = MatZeroRowsIS(B,is,diag,NULL,NULL);CHKERRQ(ierr); b = b2 = x = NULL; } else { ierr = PetscPrintf(PETSC_COMM_WORLD,"Skipping MatZeroRows (diag %s)\n",diagstr);CHKERRQ(ierr); b = b2 = x = NULL; } if (squaretest && haszerorows) { ierr = VecAXPY(b2,-1.,b);CHKERRQ(ierr); ierr = VecNorm(b2,NORM_INFINITY,&error);CHKERRQ(ierr); if (error > PETSC_SQRT_MACHINE_EPSILON) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"ERROR IN ZEROROWS ON B %g (diag %s)",error,diagstr); } /* test MatMissingDiagonal */ ierr = PetscPrintf(PETSC_COMM_WORLD,"Test MatMissingDiagonal\n");CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = MatMissingDiagonal(B,&miss,&d);CHKERRQ(ierr); ierr = MatGetOwnershipRange(B,&rst,&ren);CHKERRQ(ierr); ierr = PetscViewerASCIIPushSynchronized(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(PETSC_VIEWER_STDOUT_WORLD, "[%d] [%D,%D) Missing %d, row %D (diag %s)\n",rank,rst,ren,(int)miss,d,diagstr);CHKERRQ(ierr); ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscViewerASCIIPopSynchronized(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = VecDestroy(&b2);CHKERRQ(ierr); /* check the result of ZeroRows with that from MPIAIJ routines assuming that MatConvert_IS_XAIJ and MatZeroRows_MPIAIJ work fine */ if (haszerorows) { ierr = MatDuplicate(Afull,MAT_COPY_VALUES,&Bcheck);CHKERRQ(ierr); ierr = MatSetOption(Bcheck,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); ierr = MatZeroRowsIS(Bcheck,is,diag,NULL,NULL);CHKERRQ(ierr); ierr = CheckMat(B,Bcheck,PETSC_FALSE,"Zerorows");CHKERRQ(ierr); ierr = MatDestroy(&Bcheck);CHKERRQ(ierr); } ierr = MatDestroy(&B);CHKERRQ(ierr); if (B2) { /* test MatZeroRowsColumns */ ierr = MatDuplicate(Afull,MAT_COPY_VALUES,&B);CHKERRQ(ierr); ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); ierr = MatZeroRowsColumnsIS(B,is,diag,NULL,NULL);CHKERRQ(ierr); ierr = CheckMat(B2,B,PETSC_FALSE,"MatZeroRowsColumns");CHKERRQ(ierr); ierr = MatDestroy(&B);CHKERRQ(ierr); ierr = MatDestroy(&B2);CHKERRQ(ierr); } PetscFunctionReturn(0); }
PetscErrorCode MatLUFactorSymbolic_SeqBAIJ_inplace(Mat B,Mat A,IS isrow,IS iscol,const MatFactorInfo *info) { Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b; PetscInt n =a->mbs,bs = A->rmap->bs,bs2=a->bs2; PetscBool row_identity,col_identity,both_identity; IS isicol; PetscErrorCode ierr; const PetscInt *r,*ic; PetscInt i,*ai=a->i,*aj=a->j; PetscInt *bi,*bj,*ajtmp; PetscInt *bdiag,row,nnz,nzi,reallocs=0,nzbd,*im; PetscReal f; PetscInt nlnk,*lnk,k,**bi_ptr; PetscFreeSpaceList free_space=NULL,current_space=NULL; PetscBT lnkbt; PetscBool missing; PetscFunctionBegin; if (A->rmap->N != A->cmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"matrix must be square"); ierr = MatMissingDiagonal(A,&missing,&i);CHKERRQ(ierr); if (missing) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Matrix is missing diagonal entry %D",i); ierr = ISInvertPermutation(iscol,PETSC_DECIDE,&isicol);CHKERRQ(ierr); ierr = ISGetIndices(isrow,&r);CHKERRQ(ierr); ierr = ISGetIndices(isicol,&ic);CHKERRQ(ierr); /* get new row and diagonal pointers, must be allocated separately because they will be given to the Mat_SeqAIJ and freed separately */ ierr = PetscMalloc1(n+1,&bi);CHKERRQ(ierr); ierr = PetscMalloc1(n+1,&bdiag);CHKERRQ(ierr); bi[0] = bdiag[0] = 0; /* linked list for storing column indices of the active row */ nlnk = n + 1; ierr = PetscLLCreate(n,n,nlnk,lnk,lnkbt);CHKERRQ(ierr); ierr = PetscMalloc2(n+1,&bi_ptr,n+1,&im);CHKERRQ(ierr); /* initial FreeSpace size is f*(ai[n]+1) */ f = info->fill; ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(f,ai[n]+1),&free_space);CHKERRQ(ierr); current_space = free_space; for (i=0; i<n; i++) { /* copy previous fill into linked list */ nzi = 0; nnz = ai[r[i]+1] - ai[r[i]]; ajtmp = aj + ai[r[i]]; ierr = PetscLLAddPerm(nnz,ajtmp,ic,n,nlnk,lnk,lnkbt);CHKERRQ(ierr); nzi += nlnk; /* add pivot rows into linked list */ row = lnk[n]; while (row < i) { nzbd = bdiag[row] - bi[row] + 1; /* num of entries in the row with column index <= row */ ajtmp = bi_ptr[row] + nzbd; /* points to the entry next to the diagonal */ ierr = PetscLLAddSortedLU(ajtmp,row,nlnk,lnk,lnkbt,i,nzbd,im);CHKERRQ(ierr); nzi += nlnk; row = lnk[row]; } bi[i+1] = bi[i] + nzi; im[i] = nzi; /* mark bdiag */ nzbd = 0; nnz = nzi; k = lnk[n]; while (nnz-- && k < i) { nzbd++; k = lnk[k]; } bdiag[i] = bi[i] + nzbd; /* if free space is not available, make more free space */ if (current_space->local_remaining<nzi) { nnz = PetscIntMultTruncate(n - i,nzi); /* estimated and max additional space needed */ ierr = PetscFreeSpaceGet(nnz,¤t_space);CHKERRQ(ierr); reallocs++; } /* copy data into free space, then initialize lnk */ ierr = PetscLLClean(n,n,nzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); bi_ptr[i] = current_space->array; current_space->array += nzi; current_space->local_used += nzi; current_space->local_remaining -= nzi; } #if defined(PETSC_USE_INFO) if (ai[n] != 0) { PetscReal af = ((PetscReal)bi[n])/((PetscReal)ai[n]); ierr = PetscInfo3(A,"Reallocs %D Fill ratio:given %g needed %g\n",reallocs,(double)f,(double)af);CHKERRQ(ierr); ierr = PetscInfo1(A,"Run with -pc_factor_fill %g or use \n",(double)af);CHKERRQ(ierr); ierr = PetscInfo1(A,"PCFactorSetFill(pc,%g);\n",(double)af);CHKERRQ(ierr); ierr = PetscInfo(A,"for best performance.\n");CHKERRQ(ierr); } else { ierr = PetscInfo(A,"Empty matrix\n");CHKERRQ(ierr); } #endif ierr = ISRestoreIndices(isrow,&r);CHKERRQ(ierr); ierr = ISRestoreIndices(isicol,&ic);CHKERRQ(ierr); /* destroy list of free space and other temporary array(s) */ ierr = PetscMalloc1(bi[n]+1,&bj);CHKERRQ(ierr); ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); ierr = PetscFree2(bi_ptr,im);CHKERRQ(ierr); /* put together the new matrix */ ierr = MatSeqBAIJSetPreallocation_SeqBAIJ(B,bs,MAT_SKIP_ALLOCATION,NULL);CHKERRQ(ierr); ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)isicol);CHKERRQ(ierr); b = (Mat_SeqBAIJ*)(B)->data; b->free_a = PETSC_TRUE; b->free_ij = PETSC_TRUE; b->singlemalloc = PETSC_FALSE; ierr = PetscMalloc1((bi[n]+1)*bs2,&b->a);CHKERRQ(ierr); b->j = bj; b->i = bi; b->diag = bdiag; b->free_diag = PETSC_TRUE; b->ilen = 0; b->imax = 0; b->row = isrow; b->col = iscol; b->pivotinblocks = (info->pivotinblocks) ? PETSC_TRUE : PETSC_FALSE; ierr = PetscObjectReference((PetscObject)isrow);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject)iscol);CHKERRQ(ierr); b->icol = isicol; ierr = PetscMalloc1(bs*n+bs,&b->solve_work);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)B,(bi[n]-n)*(sizeof(PetscInt)+sizeof(PetscScalar)*bs2));CHKERRQ(ierr); b->maxnz = b->nz = bi[n]; (B)->factortype = MAT_FACTOR_LU; (B)->info.factor_mallocs = reallocs; (B)->info.fill_ratio_given = f; if (ai[n] != 0) { (B)->info.fill_ratio_needed = ((PetscReal)bi[n])/((PetscReal)ai[n]); } else { (B)->info.fill_ratio_needed = 0.0; } ierr = ISIdentity(isrow,&row_identity);CHKERRQ(ierr); ierr = ISIdentity(iscol,&col_identity);CHKERRQ(ierr); both_identity = (PetscBool) (row_identity && col_identity); ierr = MatSeqBAIJSetNumericFactorization_inplace(B,both_identity);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode MatICCFactorSymbolic_SeqAIJ_Bas(Mat fact,Mat A,IS perm,const MatFactorInfo *info) { Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; Mat_SeqSBAIJ *b; PetscErrorCode ierr; PetscBool perm_identity,missing; PetscInt reallocs=0,i,*ai=a->i,*aj=a->j,am=A->rmap->n,*ui; const PetscInt *rip,*riip; PetscInt j; PetscInt d; PetscInt ncols,*cols,*uj; PetscReal fill=info->fill,levels=info->levels; IS iperm; spbas_matrix Pattern_0, Pattern_P; PetscFunctionBegin; if (A->rmap->n != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Must be square matrix, rows %D columns %D",A->rmap->n,A->cmap->n); ierr = MatMissingDiagonal(A,&missing,&d);CHKERRQ(ierr); if (missing) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Matrix is missing diagonal entry %D",d); ierr = ISIdentity(perm,&perm_identity);CHKERRQ(ierr); ierr = ISInvertPermutation(perm,PETSC_DECIDE,&iperm);CHKERRQ(ierr); /* ICC(0) without matrix ordering: simply copies fill pattern */ if (!levels && perm_identity) { ierr = PetscMalloc1(am+1,&ui);CHKERRQ(ierr); ui[0] = 0; for (i=0; i<am; i++) { ui[i+1] = ui[i] + ai[i+1] - a->diag[i]; } ierr = PetscMalloc1(ui[am]+1,&uj);CHKERRQ(ierr); cols = uj; for (i=0; i<am; i++) { aj = a->j + a->diag[i]; ncols = ui[i+1] - ui[i]; for (j=0; j<ncols; j++) *cols++ = *aj++; } } else { /* case: levels>0 || (levels=0 && !perm_identity) */ ierr = ISGetIndices(iperm,&riip);CHKERRQ(ierr); ierr = ISGetIndices(perm,&rip);CHKERRQ(ierr); /* Create spbas_matrix for pattern */ ierr = spbas_pattern_only(am, am, ai, aj, &Pattern_0);CHKERRQ(ierr); /* Apply the permutation */ ierr = spbas_apply_reordering(&Pattern_0, rip, riip);CHKERRQ(ierr); /* Raise the power */ ierr = spbas_power(Pattern_0, (int) levels+1, &Pattern_P);CHKERRQ(ierr); ierr = spbas_delete(Pattern_0);CHKERRQ(ierr); /* Keep only upper triangle of pattern */ ierr = spbas_keep_upper(&Pattern_P);CHKERRQ(ierr); /* Convert to Sparse Row Storage */ ierr = spbas_matrix_to_crs(Pattern_P, NULL, &ui, &uj);CHKERRQ(ierr); ierr = spbas_delete(Pattern_P);CHKERRQ(ierr); } /* end of case: levels>0 || (levels=0 && !perm_identity) */ /* put together the new matrix in MATSEQSBAIJ format */ b = (Mat_SeqSBAIJ*)(fact)->data; b->singlemalloc = PETSC_FALSE; ierr = PetscMalloc1(ui[am]+1,&b->a);CHKERRQ(ierr); b->j = uj; b->i = ui; b->diag = 0; b->ilen = 0; b->imax = 0; b->row = perm; b->col = perm; ierr = PetscObjectReference((PetscObject)perm);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject)perm);CHKERRQ(ierr); b->icol = iperm; b->pivotinblocks = PETSC_FALSE; /* need to get from MatFactorInfo */ ierr = PetscMalloc1(am+1,&b->solve_work);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)(fact),(ui[am]-am)*(sizeof(PetscInt)+sizeof(MatScalar)));CHKERRQ(ierr); b->maxnz = b->nz = ui[am]; b->free_a = PETSC_TRUE; b->free_ij = PETSC_TRUE; (fact)->info.factor_mallocs = reallocs; (fact)->info.fill_ratio_given = fill; if (ai[am] != 0) { (fact)->info.fill_ratio_needed = ((PetscReal)ui[am])/((PetscReal)ai[am]); } else { (fact)->info.fill_ratio_needed = 0.0; } /* (fact)->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqAIJ_inplace; */ PetscFunctionReturn(0); }