PETSC_EXTERN PetscErrorCode MatConvert_SeqAIJ_SeqBAIJ(Mat A,MatType newtype,MatReuse reuse,Mat *newmat)
{
Mat B;
Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;
Mat_SeqBAIJ *b;
PetscErrorCode ierr;
PetscInt *ai=a->i,m=A->rmap->N,n=A->cmap->N,i,*rowlengths;
PetscFunctionBegin;
if (n != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Matrix must be square");
if (A->rmap->bs > 1) {
ierr = MatConvert_Basic(A,newtype,reuse,newmat);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
ierr = PetscMalloc1(m,&rowlengths);
CHKERRQ(ierr);
for (i=0; i<m; i++) {
rowlengths[i] = ai[i+1] - ai[i];
}
ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);
CHKERRQ(ierr);
ierr = MatSetSizes(B,m,n,m,n);
CHKERRQ(ierr);
ierr = MatSetType(B,MATSEQBAIJ);
CHKERRQ(ierr);
ierr = MatSeqBAIJSetPreallocation_SeqBAIJ(B,1,0,rowlengths);
CHKERRQ(ierr);
ierr = PetscFree(rowlengths);
CHKERRQ(ierr);
ierr = MatSetOption(B,MAT_ROW_ORIENTED,PETSC_TRUE);
CHKERRQ(ierr);
b = (Mat_SeqBAIJ*)(B->data);
ierr = PetscMemcpy(b->i,a->i,(m+1)*sizeof(PetscInt));
CHKERRQ(ierr);
ierr = PetscMemcpy(b->ilen,a->ilen,m*sizeof(PetscInt));
CHKERRQ(ierr);
ierr = PetscMemcpy(b->j,a->j,a->nz*sizeof(PetscInt));
CHKERRQ(ierr);
ierr = PetscMemcpy(b->a,a->a,a->nz*sizeof(MatScalar));
CHKERRQ(ierr);
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
if (reuse == MAT_REUSE_MATRIX) {
ierr = MatHeaderReplace(A,B);
CHKERRQ(ierr);
} else {
*newmat = B;
}
PetscFunctionReturn(0);
}
PetscErrorCode MatCreateSeqBSTRM(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatCreate(comm,A);CHKERRQ(ierr);
ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr);
ierr = MatSetType(*A,MATSEQBSTRM);CHKERRQ(ierr);
ierr = MatSeqBAIJSetPreallocation_SeqBAIJ(*A,bs,nz,(PetscInt*)nnz);CHKERRQ(ierr);
(*A)->rmap->bs = bs;
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);
}
