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);
}
