impls/nest/matnest.c

#include <../src/mat/impls/nest/matnestimpl.h> /*I   "petscmat.h"   I*/
#include <petscsf.h>

static PetscErrorCode MatSetUp_NestIS_Private(Mat,PetscInt,const IS[],PetscInt,const IS[]);
static PetscErrorCode MatCreateVecs_Nest(Mat A,Vec *right,Vec *left);

/* private functions */
#undef __FUNCT__
#define __FUNCT__ "MatNestGetSizes_Private"
static PetscErrorCode MatNestGetSizes_Private(Mat A,PetscInt *m,PetscInt *n,PetscInt *M,PetscInt *N)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  PetscInt       i,j;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  *m = *n = *M = *N = 0;
  for (i=0; i<bA->nr; i++) {  /* rows */
    PetscInt sm,sM;
    ierr = ISGetLocalSize(bA->isglobal.row[i],&sm);CHKERRQ(ierr);
    ierr = ISGetSize(bA->isglobal.row[i],&sM);CHKERRQ(ierr);
    *m  += sm;
    *M  += sM;
  }
  for (j=0; j<bA->nc; j++) {  /* cols */
    PetscInt sn,sN;
    ierr = ISGetLocalSize(bA->isglobal.col[j],&sn);CHKERRQ(ierr);
    ierr = ISGetSize(bA->isglobal.col[j],&sN);CHKERRQ(ierr);
    *n  += sn;
    *N  += sN;
  }
  PetscFunctionReturn(0);
}

/* operations */
#undef __FUNCT__
#define __FUNCT__ "MatMult_Nest"
static PetscErrorCode MatMult_Nest(Mat A,Vec x,Vec y)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  Vec            *bx = bA->right,*by = bA->left;
  PetscInt       i,j,nr = bA->nr,nc = bA->nc;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  for (i=0; i<nr; i++) {ierr = VecGetSubVector(y,bA->isglobal.row[i],&by[i]);CHKERRQ(ierr);}
  for (i=0; i<nc; i++) {ierr = VecGetSubVector(x,bA->isglobal.col[i],&bx[i]);CHKERRQ(ierr);}
  for (i=0; i<nr; i++) {
    ierr = VecZeroEntries(by[i]);CHKERRQ(ierr);
    for (j=0; j<nc; j++) {
      if (!bA->m[i][j]) continue;
      /* y[i] <- y[i] + A[i][j] * x[j] */
      ierr = MatMultAdd(bA->m[i][j],bx[j],by[i],by[i]);CHKERRQ(ierr);
    }
  }
  for (i=0; i<nr; i++) {ierr = VecRestoreSubVector(y,bA->isglobal.row[i],&by[i]);CHKERRQ(ierr);}
  for (i=0; i<nc; i++) {ierr = VecRestoreSubVector(x,bA->isglobal.col[i],&bx[i]);CHKERRQ(ierr);}
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatMultAdd_Nest"
static PetscErrorCode MatMultAdd_Nest(Mat A,Vec x,Vec y,Vec z)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  Vec            *bx = bA->right,*bz = bA->left;
  PetscInt       i,j,nr = bA->nr,nc = bA->nc;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  for (i=0; i<nr; i++) {ierr = VecGetSubVector(z,bA->isglobal.row[i],&bz[i]);CHKERRQ(ierr);}
  for (i=0; i<nc; i++) {ierr = VecGetSubVector(x,bA->isglobal.col[i],&bx[i]);CHKERRQ(ierr);}
  for (i=0; i<nr; i++) {
    if (y != z) {
      Vec by;
      ierr = VecGetSubVector(y,bA->isglobal.row[i],&by);CHKERRQ(ierr);
      ierr = VecCopy(by,bz[i]);CHKERRQ(ierr);
      ierr = VecRestoreSubVector(y,bA->isglobal.row[i],&by);CHKERRQ(ierr);
    }
    for (j=0; j<nc; j++) {
      if (!bA->m[i][j]) continue;
      /* y[i] <- y[i] + A[i][j] * x[j] */
      ierr = MatMultAdd(bA->m[i][j],bx[j],bz[i],bz[i]);CHKERRQ(ierr);
    }
  }
  for (i=0; i<nr; i++) {ierr = VecRestoreSubVector(z,bA->isglobal.row[i],&bz[i]);CHKERRQ(ierr);}
  for (i=0; i<nc; i++) {ierr = VecRestoreSubVector(x,bA->isglobal.col[i],&bx[i]);CHKERRQ(ierr);}
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatMultTranspose_Nest"
static PetscErrorCode MatMultTranspose_Nest(Mat A,Vec x,Vec y)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  Vec            *bx = bA->left,*by = bA->right;
  PetscInt       i,j,nr = bA->nr,nc = bA->nc;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  for (i=0; i<nr; i++) {ierr = VecGetSubVector(x,bA->isglobal.row[i],&bx[i]);CHKERRQ(ierr);}
  for (i=0; i<nc; i++) {ierr = VecGetSubVector(y,bA->isglobal.col[i],&by[i]);CHKERRQ(ierr);}
  for (j=0; j<nc; j++) {
    ierr = VecZeroEntries(by[j]);CHKERRQ(ierr);
    for (i=0; i<nr; i++) {
      if (!bA->m[i][j]) continue;
      /* y[j] <- y[j] + (A[i][j])^T * x[i] */
      ierr = MatMultTransposeAdd(bA->m[i][j],bx[i],by[j],by[j]);CHKERRQ(ierr);
    }
  }
  for (i=0; i<nr; i++) {ierr = VecRestoreSubVector(x,bA->isglobal.row[i],&bx[i]);CHKERRQ(ierr);}
  for (i=0; i<nc; i++) {ierr = VecRestoreSubVector(y,bA->isglobal.col[i],&by[i]);CHKERRQ(ierr);}
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatMultTransposeAdd_Nest"
static PetscErrorCode MatMultTransposeAdd_Nest(Mat A,Vec x,Vec y,Vec z)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  Vec            *bx = bA->left,*bz = bA->right;
  PetscInt       i,j,nr = bA->nr,nc = bA->nc;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  for (i=0; i<nr; i++) {ierr = VecGetSubVector(x,bA->isglobal.row[i],&bx[i]);CHKERRQ(ierr);}
  for (i=0; i<nc; i++) {ierr = VecGetSubVector(z,bA->isglobal.col[i],&bz[i]);CHKERRQ(ierr);}
  for (j=0; j<nc; j++) {
    if (y != z) {
      Vec by;
      ierr = VecGetSubVector(y,bA->isglobal.col[j],&by);CHKERRQ(ierr);
      ierr = VecCopy(by,bz[j]);CHKERRQ(ierr);
      ierr = VecRestoreSubVector(y,bA->isglobal.col[j],&by);CHKERRQ(ierr);
    }
    for (i=0; i<nr; i++) {
      if (!bA->m[i][j]) continue;
      /* z[j] <- y[j] + (A[i][j])^T * x[i] */
      ierr = MatMultTransposeAdd(bA->m[i][j],bx[i],bz[j],bz[j]);CHKERRQ(ierr);
    }
  }
  for (i=0; i<nr; i++) {ierr = VecRestoreSubVector(x,bA->isglobal.row[i],&bx[i]);CHKERRQ(ierr);}
  for (i=0; i<nc; i++) {ierr = VecRestoreSubVector(z,bA->isglobal.col[i],&bz[i]);CHKERRQ(ierr);}
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestDestroyISList"
static PetscErrorCode MatNestDestroyISList(PetscInt n,IS **list)
{
  PetscErrorCode ierr;
  IS             *lst = *list;
  PetscInt       i;

  PetscFunctionBegin;
  if (!lst) PetscFunctionReturn(0);
  for (i=0; i<n; i++) if (lst[i]) {ierr = ISDestroy(&lst[i]);CHKERRQ(ierr);}
  ierr  = PetscFree(lst);CHKERRQ(ierr);
  *list = NULL;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatDestroy_Nest"
static PetscErrorCode MatDestroy_Nest(Mat A)
{
  Mat_Nest       *vs = (Mat_Nest*)A->data;
  PetscInt       i,j;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  /* release the matrices and the place holders */
  ierr = MatNestDestroyISList(vs->nr,&vs->isglobal.row);CHKERRQ(ierr);
  ierr = MatNestDestroyISList(vs->nc,&vs->isglobal.col);CHKERRQ(ierr);
  ierr = MatNestDestroyISList(vs->nr,&vs->islocal.row);CHKERRQ(ierr);
  ierr = MatNestDestroyISList(vs->nc,&vs->islocal.col);CHKERRQ(ierr);

  ierr = PetscFree(vs->row_len);CHKERRQ(ierr);
  ierr = PetscFree(vs->col_len);CHKERRQ(ierr);

  ierr = PetscFree2(vs->left,vs->right);CHKERRQ(ierr);

  /* release the matrices and the place holders */
  if (vs->m) {
    for (i=0; i<vs->nr; i++) {
      for (j=0; j<vs->nc; j++) {
        ierr = MatDestroy(&vs->m[i][j]);CHKERRQ(ierr);
      }
      ierr = PetscFree(vs->m[i]);CHKERRQ(ierr);
    }
    ierr = PetscFree(vs->m);CHKERRQ(ierr);
  }
  ierr = PetscFree(A->data);CHKERRQ(ierr);

  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestGetSubMat_C",0);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestSetSubMat_C",0);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestGetSubMats_C",0);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestGetSize_C",0);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestGetISs_C",0);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestGetLocalISs_C",0);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestSetVecType_C",0);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestSetSubMats_C",0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatAssemblyBegin_Nest"
static PetscErrorCode MatAssemblyBegin_Nest(Mat A,MatAssemblyType type)
{
  Mat_Nest       *vs = (Mat_Nest*)A->data;
  PetscInt       i,j;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  for (i=0; i<vs->nr; i++) {
    for (j=0; j<vs->nc; j++) {
      if (vs->m[i][j]) {
        ierr = MatAssemblyBegin(vs->m[i][j],type);CHKERRQ(ierr);
        if (!vs->splitassembly) {
          /* Note: split assembly will fail if the same block appears more than once (even indirectly through a nested
           * sub-block). This could be fixed by adding a flag to Mat so that there was a way to check if a Mat was
           * already performing an assembly, but the result would by more complicated and appears to offer less
           * potential for diagnostics and correctness checking. Split assembly should be fixed once there is an
           * interface for libraries to make asynchronous progress in "user-defined non-blocking collectives".
           */
          ierr = MatAssemblyEnd(vs->m[i][j],type);CHKERRQ(ierr);
        }
      }
    }
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatAssemblyEnd_Nest"
static PetscErrorCode MatAssemblyEnd_Nest(Mat A, MatAssemblyType type)
{
  Mat_Nest       *vs = (Mat_Nest*)A->data;
  PetscInt       i,j;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  for (i=0; i<vs->nr; i++) {
    for (j=0; j<vs->nc; j++) {
      if (vs->m[i][j]) {
        if (vs->splitassembly) {
          ierr = MatAssemblyEnd(vs->m[i][j],type);CHKERRQ(ierr);
        }
      }
    }
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestFindNonzeroSubMatRow"
static PetscErrorCode MatNestFindNonzeroSubMatRow(Mat A,PetscInt row,Mat *B)
{
  PetscErrorCode ierr;
  Mat_Nest       *vs = (Mat_Nest*)A->data;
  PetscInt       j;
  Mat            sub;

  PetscFunctionBegin;
  sub = (row < vs->nc) ? vs->m[row][row] : (Mat)NULL; /* Prefer to find on the diagonal */
  for (j=0; !sub && j<vs->nc; j++) sub = vs->m[row][j];
  if (sub) {ierr = MatSetUp(sub);CHKERRQ(ierr);}       /* Ensure that the sizes are available */
  *B = sub;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestFindNonzeroSubMatCol"
static PetscErrorCode MatNestFindNonzeroSubMatCol(Mat A,PetscInt col,Mat *B)
{
  PetscErrorCode ierr;
  Mat_Nest       *vs = (Mat_Nest*)A->data;
  PetscInt       i;
  Mat            sub;

  PetscFunctionBegin;
  sub = (col < vs->nr) ? vs->m[col][col] : (Mat)NULL; /* Prefer to find on the diagonal */
  for (i=0; !sub && i<vs->nr; i++) sub = vs->m[i][col];
  if (sub) {ierr = MatSetUp(sub);CHKERRQ(ierr);}       /* Ensure that the sizes are available */
  *B = sub;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestFindIS"
static PetscErrorCode MatNestFindIS(Mat A,PetscInt n,const IS list[],IS is,PetscInt *found)
{
  PetscErrorCode ierr;
  PetscInt       i;
  PetscBool      flg;

  PetscFunctionBegin;
  PetscValidPointer(list,3);
  PetscValidHeaderSpecific(is,IS_CLASSID,4);
  PetscValidIntPointer(found,5);
  *found = -1;
  for (i=0; i<n; i++) {
    if (!list[i]) continue;
    ierr = ISEqual(list[i],is,&flg);CHKERRQ(ierr);
    if (flg) {
      *found = i;
      PetscFunctionReturn(0);
    }
  }
  SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_INCOMP,"Could not find index set");
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestGetRow"
/* Get a block row as a new MatNest */
static PetscErrorCode MatNestGetRow(Mat A,PetscInt row,Mat *B)
{
  Mat_Nest       *vs = (Mat_Nest*)A->data;
  char           keyname[256];
  PetscErrorCode ierr;

  PetscFunctionBegin;
  *B   = NULL;
  ierr = PetscSNPrintf(keyname,sizeof(keyname),"NestRow_%D",row);CHKERRQ(ierr);
  ierr = PetscObjectQuery((PetscObject)A,keyname,(PetscObject*)B);CHKERRQ(ierr);
  if (*B) PetscFunctionReturn(0);

  ierr = MatCreateNest(PetscObjectComm((PetscObject)A),1,NULL,vs->nc,vs->isglobal.col,vs->m[row],B);CHKERRQ(ierr);

  (*B)->assembled = A->assembled;

  ierr = PetscObjectCompose((PetscObject)A,keyname,(PetscObject)*B);CHKERRQ(ierr);
  ierr = PetscObjectDereference((PetscObject)*B);CHKERRQ(ierr); /* Leave the only remaining reference in the composition */
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestFindSubMat"
static PetscErrorCode MatNestFindSubMat(Mat A,struct MatNestISPair *is,IS isrow,IS iscol,Mat *B)
{
  Mat_Nest       *vs = (Mat_Nest*)A->data;
  PetscErrorCode ierr;
  PetscInt       row,col;
  PetscBool      same,isFullCol,isFullColGlobal;

  PetscFunctionBegin;
  /* Check if full column space. This is a hack */
  isFullCol = PETSC_FALSE;
  ierr      = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&same);CHKERRQ(ierr);
  if (same) {
    PetscInt n,first,step,i,an,am,afirst,astep;
    ierr      = ISStrideGetInfo(iscol,&first,&step);CHKERRQ(ierr);
    ierr      = ISGetLocalSize(iscol,&n);CHKERRQ(ierr);
    isFullCol = PETSC_TRUE;
    for (i=0,an=A->cmap->rstart; i<vs->nc; i++) {
      ierr = ISStrideGetInfo(is->col[i],&afirst,&astep);CHKERRQ(ierr);
      ierr = ISGetLocalSize(is->col[i],&am);CHKERRQ(ierr);
      if (afirst != an || astep != step) isFullCol = PETSC_FALSE;
      an += am;
    }
    if (an != A->cmap->rstart+n) isFullCol = PETSC_FALSE;
  }
  ierr = MPIU_Allreduce(&isFullCol,&isFullColGlobal,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)iscol));CHKERRQ(ierr);

  if (isFullColGlobal) {
    PetscInt row;
    ierr = MatNestFindIS(A,vs->nr,is->row,isrow,&row);CHKERRQ(ierr);
    ierr = MatNestGetRow(A,row,B);CHKERRQ(ierr);
  } else {
    ierr = MatNestFindIS(A,vs->nr,is->row,isrow,&row);CHKERRQ(ierr);
    ierr = MatNestFindIS(A,vs->nc,is->col,iscol,&col);CHKERRQ(ierr);
    *B   = vs->m[row][col];
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatGetSubMatrix_Nest"
static PetscErrorCode MatGetSubMatrix_Nest(Mat A,IS isrow,IS iscol,MatReuse reuse,Mat *B)
{
  PetscErrorCode ierr;
  Mat_Nest       *vs = (Mat_Nest*)A->data;
  Mat            sub;

  PetscFunctionBegin;
  ierr = MatNestFindSubMat(A,&vs->isglobal,isrow,iscol,&sub);CHKERRQ(ierr);
  switch (reuse) {
  case MAT_INITIAL_MATRIX:
    if (sub) { ierr = PetscObjectReference((PetscObject)sub);CHKERRQ(ierr); }
    *B = sub;
    break;
  case MAT_REUSE_MATRIX:
    if (sub != *B) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONGSTATE,"Submatrix was not used before in this call");
    break;
  case MAT_IGNORE_MATRIX:       /* Nothing to do */
    break;
  case MAT_INPLACE_MATRIX:       /* Nothing to do */
    SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"MAT_INPLACE_MATRIX is not supported yet");
    break;
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatGetLocalSubMatrix_Nest"
PetscErrorCode MatGetLocalSubMatrix_Nest(Mat A,IS isrow,IS iscol,Mat *B)
{
  PetscErrorCode ierr;
  Mat_Nest       *vs = (Mat_Nest*)A->data;
  Mat            sub;

  PetscFunctionBegin;
  ierr = MatNestFindSubMat(A,&vs->islocal,isrow,iscol,&sub);CHKERRQ(ierr);
  /* We allow the submatrix to be NULL, perhaps it would be better for the user to return an empty matrix instead */
  if (sub) {ierr = PetscObjectReference((PetscObject)sub);CHKERRQ(ierr);}
  *B = sub;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatRestoreLocalSubMatrix_Nest"
static PetscErrorCode MatRestoreLocalSubMatrix_Nest(Mat A,IS isrow,IS iscol,Mat *B)
{
  PetscErrorCode ierr;
  Mat_Nest       *vs = (Mat_Nest*)A->data;
  Mat            sub;

  PetscFunctionBegin;
  ierr = MatNestFindSubMat(A,&vs->islocal,isrow,iscol,&sub);CHKERRQ(ierr);
  if (*B != sub) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONGSTATE,"Local submatrix has not been gotten");
  if (sub) {
    if (((PetscObject)sub)->refct <= 1) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONGSTATE,"Local submatrix has had reference count decremented too many times");
    ierr = MatDestroy(B);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatGetDiagonal_Nest"
static PetscErrorCode MatGetDiagonal_Nest(Mat A,Vec v)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  PetscInt       i;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  for (i=0; i<bA->nr; i++) {
    Vec bv;
    ierr = VecGetSubVector(v,bA->isglobal.row[i],&bv);CHKERRQ(ierr);
    if (bA->m[i][i]) {
      ierr = MatGetDiagonal(bA->m[i][i],bv);CHKERRQ(ierr);
    } else {
      ierr = VecSet(bv,0.0);CHKERRQ(ierr);
    }
    ierr = VecRestoreSubVector(v,bA->isglobal.row[i],&bv);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatDiagonalScale_Nest"
static PetscErrorCode MatDiagonalScale_Nest(Mat A,Vec l,Vec r)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  Vec            bl,*br;
  PetscInt       i,j;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscCalloc1(bA->nc,&br);CHKERRQ(ierr);
  if (r) {
    for (j=0; j<bA->nc; j++) {ierr = VecGetSubVector(r,bA->isglobal.col[j],&br[j]);CHKERRQ(ierr);}
  }
  bl = NULL;
  for (i=0; i<bA->nr; i++) {
    if (l) {
      ierr = VecGetSubVector(l,bA->isglobal.row[i],&bl);CHKERRQ(ierr);
    }
    for (j=0; j<bA->nc; j++) {
      if (bA->m[i][j]) {
        ierr = MatDiagonalScale(bA->m[i][j],bl,br[j]);CHKERRQ(ierr);
      }
    }
    if (l) {
      ierr = VecRestoreSubVector(l,bA->isglobal.row[i],&bl);CHKERRQ(ierr);
    }
  }
  if (r) {
    for (j=0; j<bA->nc; j++) {ierr = VecRestoreSubVector(r,bA->isglobal.col[j],&br[j]);CHKERRQ(ierr);}
  }
  ierr = PetscFree(br);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatScale_Nest"
static PetscErrorCode MatScale_Nest(Mat A,PetscScalar a)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  PetscInt       i,j;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  for (i=0; i<bA->nr; i++) {
    for (j=0; j<bA->nc; j++) {
      if (bA->m[i][j]) {
        ierr = MatScale(bA->m[i][j],a);CHKERRQ(ierr);
      }
    }
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatShift_Nest"
static PetscErrorCode MatShift_Nest(Mat A,PetscScalar a)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  PetscInt       i;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  for (i=0; i<bA->nr; i++) {
    if (!bA->m[i][i]) SETERRQ2(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"No support for shifting an empty diagonal block, insert a matrix in block (%D,%D)",i,i);
    ierr = MatShift(bA->m[i][i],a);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatCreateVecs_Nest"
static PetscErrorCode MatCreateVecs_Nest(Mat A,Vec *right,Vec *left)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  Vec            *L,*R;
  MPI_Comm       comm;
  PetscInt       i,j;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr);
  if (right) {
    /* allocate R */
    ierr = PetscMalloc1(bA->nc, &R);CHKERRQ(ierr);
    /* Create the right vectors */
    for (j=0; j<bA->nc; j++) {
      for (i=0; i<bA->nr; i++) {
        if (bA->m[i][j]) {
          ierr = MatCreateVecs(bA->m[i][j],&R[j],NULL);CHKERRQ(ierr);
          break;
        }
      }
      if (i==bA->nr) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_ARG_WRONG, "Mat(Nest) contains a null column.");
    }
    ierr = VecCreateNest(comm,bA->nc,bA->isglobal.col,R,right);CHKERRQ(ierr);
    /* hand back control to the nest vector */
    for (j=0; j<bA->nc; j++) {
      ierr = VecDestroy(&R[j]);CHKERRQ(ierr);
    }
    ierr = PetscFree(R);CHKERRQ(ierr);
  }

  if (left) {
    /* allocate L */
    ierr = PetscMalloc1(bA->nr, &L);CHKERRQ(ierr);
    /* Create the left vectors */
    for (i=0; i<bA->nr; i++) {
      for (j=0; j<bA->nc; j++) {
        if (bA->m[i][j]) {
          ierr = MatCreateVecs(bA->m[i][j],NULL,&L[i]);CHKERRQ(ierr);
          break;
        }
      }
      if (j==bA->nc) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_ARG_WRONG, "Mat(Nest) contains a null row.");
    }

    ierr = VecCreateNest(comm,bA->nr,bA->isglobal.row,L,left);CHKERRQ(ierr);
    for (i=0; i<bA->nr; i++) {
      ierr = VecDestroy(&L[i]);CHKERRQ(ierr);
    }

    ierr = PetscFree(L);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatView_Nest"
static PetscErrorCode MatView_Nest(Mat A,PetscViewer viewer)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  PetscBool      isascii;
  PetscInt       i,j;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&isascii);CHKERRQ(ierr);
  if (isascii) {

    PetscViewerASCIIPrintf(viewer,"Matrix object: \n");
    PetscViewerASCIIPushTab(viewer);    /* push0 */
    PetscViewerASCIIPrintf(viewer, "type=nest, rows=%d, cols=%d \n",bA->nr,bA->nc);

    PetscViewerASCIIPrintf(viewer,"MatNest structure: \n");
    for (i=0; i<bA->nr; i++) {
      for (j=0; j<bA->nc; j++) {
        MatType   type;
        char      name[256] = "",prefix[256] = "";
        PetscInt  NR,NC;
        PetscBool isNest = PETSC_FALSE;

        if (!bA->m[i][j]) {
          PetscViewerASCIIPrintf(viewer, "(%D,%D) : NULL \n",i,j);
          continue;
        }
        ierr = MatGetSize(bA->m[i][j],&NR,&NC);CHKERRQ(ierr);
        ierr = MatGetType(bA->m[i][j], &type);CHKERRQ(ierr);
        if (((PetscObject)bA->m[i][j])->name) {ierr = PetscSNPrintf(name,sizeof(name),"name=\"%s\", ",((PetscObject)bA->m[i][j])->name);CHKERRQ(ierr);}
        if (((PetscObject)bA->m[i][j])->prefix) {ierr = PetscSNPrintf(prefix,sizeof(prefix),"prefix=\"%s\", ",((PetscObject)bA->m[i][j])->prefix);CHKERRQ(ierr);}
        ierr = PetscObjectTypeCompare((PetscObject)bA->m[i][j],MATNEST,&isNest);CHKERRQ(ierr);

        ierr = PetscViewerASCIIPrintf(viewer,"(%D,%D) : %s%stype=%s, rows=%D, cols=%D \n",i,j,name,prefix,type,NR,NC);CHKERRQ(ierr);

        if (isNest) {
          ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);  /* push1 */
          ierr = MatView(bA->m[i][j],viewer);CHKERRQ(ierr);
          ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);    /* pop1 */
        }
      }
    }
    PetscViewerASCIIPopTab(viewer);    /* pop0 */
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatZeroEntries_Nest"
static PetscErrorCode MatZeroEntries_Nest(Mat A)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  PetscInt       i,j;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  for (i=0; i<bA->nr; i++) {
    for (j=0; j<bA->nc; j++) {
      if (!bA->m[i][j]) continue;
      ierr = MatZeroEntries(bA->m[i][j]);CHKERRQ(ierr);
    }
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatCopy_Nest"
static PetscErrorCode MatCopy_Nest(Mat A,Mat B,MatStructure str)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data,*bB = (Mat_Nest*)B->data;
  PetscInt       i,j,nr = bA->nr,nc = bA->nc;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (nr != bB->nr || nc != bB->nc) SETERRQ4(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_INCOMP,"Cannot copy a Mat_Nest of block size (%D,%D) to a Mat_Nest of block size (%D,%D)",bB->nr,bB->nc,nr,nc);
  for (i=0; i<nr; i++) {
    for (j=0; j<nc; j++) {
      if (bA->m[i][j] && bB->m[i][j]) {
        ierr = MatCopy(bA->m[i][j],bB->m[i][j],str);CHKERRQ(ierr);
      } else if (bA->m[i][j] || bB->m[i][j]) SETERRQ2(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_INCOMP,"Matrix block does not exist at %D,%D",i,j);
    }
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatDuplicate_Nest"
static PetscErrorCode MatDuplicate_Nest(Mat A,MatDuplicateOption op,Mat *B)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  Mat            *b;
  PetscInt       i,j,nr = bA->nr,nc = bA->nc;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscMalloc1(nr*nc,&b);CHKERRQ(ierr);
  for (i=0; i<nr; i++) {
    for (j=0; j<nc; j++) {
      if (bA->m[i][j]) {
        ierr = MatDuplicate(bA->m[i][j],op,&b[i*nc+j]);CHKERRQ(ierr);
      } else {
        b[i*nc+j] = NULL;
      }
    }
  }
  ierr = MatCreateNest(PetscObjectComm((PetscObject)A),nr,bA->isglobal.row,nc,bA->isglobal.col,b,B);CHKERRQ(ierr);
  /* Give the new MatNest exclusive ownership */
  for (i=0; i<nr*nc; i++) {
    ierr = MatDestroy(&b[i]);CHKERRQ(ierr);
  }
  ierr = PetscFree(b);CHKERRQ(ierr);

  ierr = MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/* nest api */
#undef __FUNCT__
#define __FUNCT__ "MatNestGetSubMat_Nest"
PetscErrorCode MatNestGetSubMat_Nest(Mat A,PetscInt idxm,PetscInt jdxm,Mat *mat)
{
  Mat_Nest *bA = (Mat_Nest*)A->data;

  PetscFunctionBegin;
  if (idxm >= bA->nr) SETERRQ2(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm,bA->nr-1);
  if (jdxm >= bA->nc) SETERRQ2(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Col too large: row %D max %D",jdxm,bA->nc-1);
  *mat = bA->m[idxm][jdxm];
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestGetSubMat"
/*@
 MatNestGetSubMat - Returns a single, sub-matrix from a nest matrix.

 Not collective

 Input Parameters:
+   A  - nest matrix
.   idxm - index of the matrix within the nest matrix
-   jdxm - index of the matrix within the nest matrix

 Output Parameter:
.   sub - matrix at index idxm,jdxm within the nest matrix

 Level: developer

.seealso: MatNestGetSize(), MatNestGetSubMats()
@*/
PetscErrorCode  MatNestGetSubMat(Mat A,PetscInt idxm,PetscInt jdxm,Mat *sub)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscUseMethod(A,"MatNestGetSubMat_C",(Mat,PetscInt,PetscInt,Mat*),(A,idxm,jdxm,sub));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestSetSubMat_Nest"
PetscErrorCode MatNestSetSubMat_Nest(Mat A,PetscInt idxm,PetscInt jdxm,Mat mat)
{
  Mat_Nest       *bA = (Mat_Nest*)A->data;
  PetscInt       m,n,M,N,mi,ni,Mi,Ni;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (idxm >= bA->nr) SETERRQ2(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm,bA->nr-1);
  if (jdxm >= bA->nc) SETERRQ2(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Col too large: row %D max %D",jdxm,bA->nc-1);
  ierr = MatGetLocalSize(mat,&m,&n);CHKERRQ(ierr);
  ierr = MatGetSize(mat,&M,&N);CHKERRQ(ierr);
  ierr = ISGetLocalSize(bA->isglobal.row[idxm],&mi);CHKERRQ(ierr);
  ierr = ISGetSize(bA->isglobal.row[idxm],&Mi);CHKERRQ(ierr);
  ierr = ISGetLocalSize(bA->isglobal.col[jdxm],&ni);CHKERRQ(ierr);
  ierr = ISGetSize(bA->isglobal.col[jdxm],&Ni);CHKERRQ(ierr);
  if (M != Mi || N != Ni) SETERRQ4(PetscObjectComm((PetscObject)mat),PETSC_ERR_ARG_INCOMP,"Submatrix dimension (%D,%D) incompatible with nest block (%D,%D)",M,N,Mi,Ni);
  if (m != mi || n != ni) SETERRQ4(PetscObjectComm((PetscObject)mat),PETSC_ERR_ARG_INCOMP,"Submatrix local dimension (%D,%D) incompatible with nest block (%D,%D)",m,n,mi,ni);

  ierr = PetscObjectReference((PetscObject)mat);CHKERRQ(ierr);
  ierr = MatDestroy(&bA->m[idxm][jdxm]);CHKERRQ(ierr);
  bA->m[idxm][jdxm] = mat;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestSetSubMat"
/*@
 MatNestSetSubMat - Set a single submatrix in the nest matrix.

 Logically collective on the submatrix communicator

 Input Parameters:
+   A  - nest matrix
.   idxm - index of the matrix within the nest matrix
.   jdxm - index of the matrix within the nest matrix
-   sub - matrix at index idxm,jdxm within the nest matrix

 Notes:
 The new submatrix must have the same size and communicator as that block of the nest.

 This increments the reference count of the submatrix.

 Level: developer

.seealso: MatNestSetSubMats(), MatNestGetSubMat()
@*/
PetscErrorCode  MatNestSetSubMat(Mat A,PetscInt idxm,PetscInt jdxm,Mat sub)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscUseMethod(A,"MatNestSetSubMat_C",(Mat,PetscInt,PetscInt,Mat),(A,idxm,jdxm,sub));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestGetSubMats_Nest"
PetscErrorCode MatNestGetSubMats_Nest(Mat A,PetscInt *M,PetscInt *N,Mat ***mat)
{
  Mat_Nest *bA = (Mat_Nest*)A->data;

  PetscFunctionBegin;
  if (M)   *M   = bA->nr;
  if (N)   *N   = bA->nc;
  if (mat) *mat = bA->m;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestGetSubMats"
/*@C
 MatNestGetSubMats - Returns the entire two dimensional array of matrices defining a nest matrix.

 Not collective

 Input Parameters:
.   A  - nest matrix

 Output Parameter:
+   M - number of rows in the nest matrix
.   N - number of cols in the nest matrix
-   mat - 2d array of matrices

 Notes:

 The user should not free the array mat.

 Level: developer

.seealso: MatNestGetSize(), MatNestGetSubMat()
@*/
PetscErrorCode  MatNestGetSubMats(Mat A,PetscInt *M,PetscInt *N,Mat ***mat)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscUseMethod(A,"MatNestGetSubMats_C",(Mat,PetscInt*,PetscInt*,Mat***),(A,M,N,mat));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestGetSize_Nest"
PetscErrorCode  MatNestGetSize_Nest(Mat A,PetscInt *M,PetscInt *N)
{
  Mat_Nest *bA = (Mat_Nest*)A->data;

  PetscFunctionBegin;
  if (M) *M = bA->nr;
  if (N) *N = bA->nc;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestGetSize"
/*@
 MatNestGetSize - Returns the size of the nest matrix.

 Not collective

 Input Parameters:
.   A  - nest matrix

 Output Parameter:
+   M - number of rows in the nested mat
-   N - number of cols in the nested mat

 Notes:

 Level: developer

.seealso: MatNestGetSubMat(), MatNestGetSubMats()
@*/
PetscErrorCode  MatNestGetSize(Mat A,PetscInt *M,PetscInt *N)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscUseMethod(A,"MatNestGetSize_C",(Mat,PetscInt*,PetscInt*),(A,M,N));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestGetISs_Nest"
static PetscErrorCode MatNestGetISs_Nest(Mat A,IS rows[],IS cols[])
{
  Mat_Nest *vs = (Mat_Nest*)A->data;
  PetscInt i;

  PetscFunctionBegin;
  if (rows) for (i=0; i<vs->nr; i++) rows[i] = vs->isglobal.row[i];
  if (cols) for (i=0; i<vs->nc; i++) cols[i] = vs->isglobal.col[i];
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestGetISs"
/*@C
 MatNestGetISs - Returns the index sets partitioning the row and column spaces

 Not collective

 Input Parameters:
.   A  - nest matrix

 Output Parameter:
+   rows - array of row index sets
-   cols - array of column index sets

 Level: advanced

 Notes:
 The user must have allocated arrays of the correct size. The reference count is not increased on the returned ISs.

.seealso: MatNestGetSubMat(), MatNestGetSubMats(), MatNestGetSize(), MatNestGetLocalISs()
@*/
PetscErrorCode  MatNestGetISs(Mat A,IS rows[],IS cols[])
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(A,MAT_CLASSID,1);
  ierr = PetscUseMethod(A,"MatNestGetISs_C",(Mat,IS[],IS[]),(A,rows,cols));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestGetLocalISs_Nest"
static PetscErrorCode MatNestGetLocalISs_Nest(Mat A,IS rows[],IS cols[])
{
  Mat_Nest *vs = (Mat_Nest*)A->data;
  PetscInt i;

  PetscFunctionBegin;
  if (rows) for (i=0; i<vs->nr; i++) rows[i] = vs->islocal.row[i];
  if (cols) for (i=0; i<vs->nc; i++) cols[i] = vs->islocal.col[i];
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestGetLocalISs"
/*@C
 MatNestGetLocalISs - Returns the index sets partitioning the row and column spaces

 Not collective

 Input Parameters:
.   A  - nest matrix

 Output Parameter:
+   rows - array of row index sets (or NULL to ignore)
-   cols - array of column index sets (or NULL to ignore)

 Level: advanced

 Notes:
 The user must have allocated arrays of the correct size. The reference count is not increased on the returned ISs.

.seealso: MatNestGetSubMat(), MatNestGetSubMats(), MatNestGetSize(), MatNestGetISs()
@*/
PetscErrorCode  MatNestGetLocalISs(Mat A,IS rows[],IS cols[])
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(A,MAT_CLASSID,1);
  ierr = PetscUseMethod(A,"MatNestGetLocalISs_C",(Mat,IS[],IS[]),(A,rows,cols));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestSetVecType_Nest"
PetscErrorCode  MatNestSetVecType_Nest(Mat A,VecType vtype)
{
  PetscErrorCode ierr;
  PetscBool      flg;

  PetscFunctionBegin;
  ierr = PetscStrcmp(vtype,VECNEST,&flg);CHKERRQ(ierr);
  /* In reality, this only distinguishes VECNEST and "other" */
  if (flg) A->ops->getvecs = MatCreateVecs_Nest;
  else A->ops->getvecs = (PetscErrorCode (*)(Mat,Vec*,Vec*)) 0;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestSetVecType"
/*@C
 MatNestSetVecType - Sets the type of Vec returned by MatCreateVecs()

 Not collective

 Input Parameters:
+  A  - nest matrix
-  vtype - type to use for creating vectors

 Notes:

 Level: developer

.seealso: MatCreateVecs()
@*/
PetscErrorCode  MatNestSetVecType(Mat A,VecType vtype)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscTryMethod(A,"MatNestSetVecType_C",(Mat,VecType),(A,vtype));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestSetSubMats_Nest"
PetscErrorCode MatNestSetSubMats_Nest(Mat A,PetscInt nr,const IS is_row[],PetscInt nc,const IS is_col[],const Mat a[])
{
  Mat_Nest       *s = (Mat_Nest*)A->data;
  PetscInt       i,j,m,n,M,N;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  s->nr = nr;
  s->nc = nc;

  /* Create space for submatrices */
  ierr = PetscMalloc1(nr,&s->m);CHKERRQ(ierr);
  for (i=0; i<nr; i++) {
    ierr = PetscMalloc1(nc,&s->m[i]);CHKERRQ(ierr);
  }
  for (i=0; i<nr; i++) {
    for (j=0; j<nc; j++) {
      s->m[i][j] = a[i*nc+j];
      if (a[i*nc+j]) {
        ierr = PetscObjectReference((PetscObject)a[i*nc+j]);CHKERRQ(ierr);
      }
    }
  }

  ierr = MatSetUp_NestIS_Private(A,nr,is_row,nc,is_col);CHKERRQ(ierr);

  ierr = PetscMalloc1(nr,&s->row_len);CHKERRQ(ierr);
  ierr = PetscMalloc1(nc,&s->col_len);CHKERRQ(ierr);
  for (i=0; i<nr; i++) s->row_len[i]=-1;
  for (j=0; j<nc; j++) s->col_len[j]=-1;

  ierr = MatNestGetSizes_Private(A,&m,&n,&M,&N);CHKERRQ(ierr);

  ierr = PetscLayoutSetSize(A->rmap,M);CHKERRQ(ierr);
  ierr = PetscLayoutSetLocalSize(A->rmap,m);CHKERRQ(ierr);
  ierr = PetscLayoutSetSize(A->cmap,N);CHKERRQ(ierr);
  ierr = PetscLayoutSetLocalSize(A->cmap,n);CHKERRQ(ierr);

  ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr);
  ierr = PetscLayoutSetUp(A->cmap);CHKERRQ(ierr);

  ierr = PetscCalloc2(nr,&s->left,nc,&s->right);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestSetSubMats"
/*@
   MatNestSetSubMats - Sets the nested submatrices

   Collective on Mat

   Input Parameter:
+  N - nested matrix
.  nr - number of nested row blocks
.  is_row - index sets for each nested row block, or NULL to make contiguous
.  nc - number of nested column blocks
.  is_col - index sets for each nested column block, or NULL to make contiguous
-  a - row-aligned array of nr*nc submatrices, empty submatrices can be passed using NULL

   Level: advanced

.seealso: MatCreateNest(), MATNEST
@*/
PetscErrorCode MatNestSetSubMats(Mat A,PetscInt nr,const IS is_row[],PetscInt nc,const IS is_col[],const Mat a[])
{
  PetscErrorCode ierr;
  PetscInt       i;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(A,MAT_CLASSID,1);
  if (nr < 0) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Number of rows cannot be negative");
  if (nr && is_row) {
    PetscValidPointer(is_row,3);
    for (i=0; i<nr; i++) PetscValidHeaderSpecific(is_row[i],IS_CLASSID,3);
  }
  if (nc < 0) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Number of columns cannot be negative");
  if (nc && is_col) {
    PetscValidPointer(is_col,5);
    for (i=0; i<nc; i++) PetscValidHeaderSpecific(is_col[i],IS_CLASSID,5);
  }
  if (nr*nc) PetscValidPointer(a,6);
  ierr = PetscUseMethod(A,"MatNestSetSubMats_C",(Mat,PetscInt,const IS[],PetscInt,const IS[],const Mat[]),(A,nr,is_row,nc,is_col,a));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatNestCreateAggregateL2G_Private"
static PetscErrorCode MatNestCreateAggregateL2G_Private(Mat A,PetscInt n,const IS islocal[],const IS isglobal[],PetscBool colflg,ISLocalToGlobalMapping *ltog)
{
  PetscErrorCode ierr;
  PetscBool      flg;
  PetscInt       i,j,m,mi,*ix;

  PetscFunctionBegin;
  for (i=0,m=0,flg=PETSC_FALSE; i<n; i++) {
    if (islocal[i]) {
      ierr = ISGetSize(islocal[i],&mi);CHKERRQ(ierr);
      flg  = PETSC_TRUE;      /* We found a non-trivial entry */
    } else {
      ierr = ISGetSize(isglobal[i],&mi);CHKERRQ(ierr);
    }
    m += mi;
  }
  if (flg) {
    ierr = PetscMalloc1(m,&ix);CHKERRQ(ierr);
    for (i=0,n=0; i<n; i++) {
      ISLocalToGlobalMapping smap = NULL;
      VecScatter             scat;
      IS                     isreq;
      Vec                    lvec,gvec;
      union {char padding[sizeof(PetscScalar)]; PetscInt integer;} *x;
      Mat sub;

      if (sizeof(*x) != sizeof(PetscScalar)) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"No support when scalars smaller than integers");
      if (colflg) {
        ierr = MatNestFindNonzeroSubMatRow(A,i,&sub);CHKERRQ(ierr);
      } else {
        ierr = MatNestFindNonzeroSubMatCol(A,i,&sub);CHKERRQ(ierr);
      }
      if (sub) {ierr = MatGetLocalToGlobalMapping(sub,&smap,NULL);CHKERRQ(ierr);}
      if (islocal[i]) {
        ierr = ISGetSize(islocal[i],&mi);CHKERRQ(ierr);
      } else {
        ierr = ISGetSize(isglobal[i],&mi);CHKERRQ(ierr);
      }
      for (j=0; j<mi; j++) ix[m+j] = j;
      if (smap) {ierr = ISLocalToGlobalMappingApply(smap,mi,ix+m,ix+m);CHKERRQ(ierr);}
      /*
        Now we need to extract the monolithic global indices that correspond to the given split global indices.
        In many/most cases, we only want MatGetLocalSubMatrix() to work, in which case we only need to know the size of the local spaces.
        The approach here is ugly because it uses VecScatter to move indices.
       */
      ierr = VecCreateSeq(PETSC_COMM_SELF,mi,&lvec);CHKERRQ(ierr);
      ierr = VecCreateMPI(((PetscObject)isglobal[i])->comm,mi,PETSC_DECIDE,&gvec);CHKERRQ(ierr);
      ierr = ISCreateGeneral(((PetscObject)isglobal[i])->comm,mi,ix+m,PETSC_COPY_VALUES,&isreq);CHKERRQ(ierr);
      ierr = VecScatterCreate(gvec,isreq,lvec,NULL,&scat);CHKERRQ(ierr);
      ierr = VecGetArray(gvec,(PetscScalar**)&x);CHKERRQ(ierr);
      for (j=0; j<mi; j++) x[j].integer = ix[m+j];
      ierr = VecRestoreArray(gvec,(PetscScalar**)&x);CHKERRQ(ierr);
      ierr = VecScatterBegin(scat,gvec,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
      ierr = VecScatterEnd(scat,gvec,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
      ierr = VecGetArray(lvec,(PetscScalar**)&x);CHKERRQ(ierr);
      for (j=0; j<mi; j++) ix[m+j] = x[j].integer;
      ierr = VecRestoreArray(lvec,(PetscScalar**)&x);CHKERRQ(ierr);
      ierr = VecDestroy(&lvec);CHKERRQ(ierr);
      ierr = VecDestroy(&gvec);CHKERRQ(ierr);
      ierr = ISDestroy(&isreq);CHKERRQ(ierr);
      ierr = VecScatterDestroy(&scat);CHKERRQ(ierr);
      m   += mi;
    }
    ierr   = ISLocalToGlobalMappingCreate(PetscObjectComm((PetscObject)A),1,m,ix,PETSC_OWN_POINTER,ltog);CHKERRQ(ierr);
  } else {
    *ltog  = NULL;
  }
  PetscFunctionReturn(0);
}


/* If an IS was provided, there is nothing Nest needs to do, otherwise Nest will build a strided IS */
/*
  nprocessors = NP
  Nest x^T = ((g_0,g_1,...g_nprocs-1), (h_0,h_1,...h_NP-1))
       proc 0: => (g_0,h_0,)
       proc 1: => (g_1,h_1,)
       ...
       proc nprocs-1: => (g_NP-1,h_NP-1,)

            proc 0:                      proc 1:                    proc nprocs-1:
    is[0] = (0,1,2,...,nlocal(g_0)-1)  (0,1,...,nlocal(g_1)-1)  (0,1,...,nlocal(g_NP-1))

            proc 0:
    is[1] = (nlocal(g_0),nlocal(g_0)+1,...,nlocal(g_0)+nlocal(h_0)-1)
            proc 1:
    is[1] = (nlocal(g_1),nlocal(g_1)+1,...,nlocal(g_1)+nlocal(h_1)-1)

            proc NP-1:
    is[1] = (nlocal(g_NP-1),nlocal(g_NP-1)+1,...,nlocal(g_NP-1)+nlocal(h_NP-1)-1)
*/
#undef __FUNCT__
#define __FUNCT__ "MatSetUp_NestIS_Private"
static PetscErrorCode MatSetUp_NestIS_Private(Mat A,PetscInt nr,const IS is_row[],PetscInt nc,const IS is_col[])
{
  Mat_Nest       *vs = (Mat_Nest*)A->data;
  PetscInt       i,j,offset,n,nsum,bs;
  PetscErrorCode ierr;
  Mat            sub = NULL;

  PetscFunctionBegin;
  ierr = PetscMalloc1(nr,&vs->isglobal.row);CHKERRQ(ierr);
  ierr = PetscMalloc1(nc,&vs->isglobal.col);CHKERRQ(ierr);
  if (is_row) { /* valid IS is passed in */
    /* refs on is[] are incremeneted */
    for (i=0; i<vs->nr; i++) {
      ierr = PetscObjectReference((PetscObject)is_row[i]);CHKERRQ(ierr);

      vs->isglobal.row[i] = is_row[i];
    }
  } else {                      /* Create the ISs by inspecting sizes of a submatrix in each row */
    nsum = 0;
    for (i=0; i<vs->nr; i++) {  /* Add up the local sizes to compute the aggregate offset */
      ierr = MatNestFindNonzeroSubMatRow(A,i,&sub);CHKERRQ(ierr);
      if (!sub) SETERRQ1(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"No nonzero submatrix in row %D",i);
      ierr = MatGetLocalSize(sub,&n,NULL);CHKERRQ(ierr);
      if (n < 0) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONGSTATE,"Sizes have not yet been set for submatrix");
      nsum += n;
    }
    ierr    = MPI_Scan(&nsum,&offset,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr);
    offset -= nsum;
    for (i=0; i<vs->nr; i++) {
      ierr    = MatNestFindNonzeroSubMatRow(A,i,&sub);CHKERRQ(ierr);
      ierr    = MatGetLocalSize(sub,&n,NULL);CHKERRQ(ierr);
      ierr    = MatGetBlockSize(sub,&bs);CHKERRQ(ierr);
      ierr    = ISCreateStride(PetscObjectComm((PetscObject)sub),n,offset,1,&vs->isglobal.row[i]);CHKERRQ(ierr);
      ierr    = ISSetBlockSize(vs->isglobal.row[i],bs);CHKERRQ(ierr);
      offset += n;
    }
  }

  if (is_col) { /* valid IS is passed in */
    /* refs on is[] are incremeneted */
    for (j=0; j<vs->nc; j++) {
      ierr = PetscObjectReference((PetscObject)is_col[j]);CHKERRQ(ierr);

      vs->isglobal.col[j] = is_col[j];
    }
  } else {                      /* Create the ISs by inspecting sizes of a submatrix in each column */
    offset = A->cmap->rstart;
    nsum   = 0;
    for (j=0; j<vs->nc; j++) {
      ierr = MatNestFindNonzeroSubMatCol(A,j,&sub);CHKERRQ(ierr);
      if (!sub) SETERRQ1(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"No nonzero submatrix in column %D",i);
      ierr = MatGetLocalSize(sub,NULL,&n);CHKERRQ(ierr);
      if (n < 0) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONGSTATE,"Sizes have not yet been set for submatrix");
      nsum += n;
    }
    ierr    = MPI_Scan(&nsum,&offset,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr);
    offset -= nsum;
    for (j=0; j<vs->nc; j++) {
      ierr    = MatNestFindNonzeroSubMatCol(A,j,&sub);CHKERRQ(ierr);
      ierr    = MatGetLocalSize(sub,NULL,&n);CHKERRQ(ierr);
      ierr    = MatGetBlockSize(sub,&bs);CHKERRQ(ierr);
      ierr    = ISCreateStride(PetscObjectComm((PetscObject)sub),n,offset,1,&vs->isglobal.col[j]);CHKERRQ(ierr);
      ierr    = ISSetBlockSize(vs->isglobal.col[j],bs);CHKERRQ(ierr);
      offset += n;
    }
  }

  /* Set up the local ISs */
  ierr = PetscMalloc1(vs->nr,&vs->islocal.row);CHKERRQ(ierr);
  ierr = PetscMalloc1(vs->nc,&vs->islocal.col);CHKERRQ(ierr);
  for (i=0,offset=0; i<vs->nr; i++) {
    IS                     isloc;
    ISLocalToGlobalMapping rmap = NULL;
    PetscInt               nlocal,bs;
    ierr = MatNestFindNonzeroSubMatRow(A,i,&sub);CHKERRQ(ierr);
    if (sub) {ierr = MatGetLocalToGlobalMapping(sub,&rmap,NULL);CHKERRQ(ierr);}
    if (rmap) {
      ierr = MatGetBlockSize(sub,&bs);CHKERRQ(ierr);
      ierr = ISLocalToGlobalMappingGetSize(rmap,&nlocal);CHKERRQ(ierr);
      ierr = ISCreateStride(PETSC_COMM_SELF,nlocal,offset,1,&isloc);CHKERRQ(ierr);
      ierr = ISSetBlockSize(isloc,bs);CHKERRQ(ierr);
    } else {
      nlocal = 0;
      isloc  = NULL;
    }
    vs->islocal.row[i] = isloc;
    offset            += nlocal;
  }
  for (i=0,offset=0; i<vs->nc; i++) {
    IS                     isloc;
    ISLocalToGlobalMapping cmap = NULL;
    PetscInt               nlocal,bs;
    ierr = MatNestFindNonzeroSubMatCol(A,i,&sub);CHKERRQ(ierr);
    if (sub) {ierr = MatGetLocalToGlobalMapping(sub,NULL,&cmap);CHKERRQ(ierr);}
    if (cmap) {
      ierr = MatGetBlockSize(sub,&bs);CHKERRQ(ierr);
      ierr = ISLocalToGlobalMappingGetSize(cmap,&nlocal);CHKERRQ(ierr);
      ierr = ISCreateStride(PETSC_COMM_SELF,nlocal,offset,1,&isloc);CHKERRQ(ierr);
      ierr = ISSetBlockSize(isloc,bs);CHKERRQ(ierr);
    } else {
      nlocal = 0;
      isloc  = NULL;
    }
    vs->islocal.col[i] = isloc;
    offset            += nlocal;
  }

  /* Set up the aggregate ISLocalToGlobalMapping */
  {
    ISLocalToGlobalMapping rmap,cmap;
    ierr = MatNestCreateAggregateL2G_Private(A,vs->nr,vs->islocal.row,vs->isglobal.row,PETSC_FALSE,&rmap);CHKERRQ(ierr);
    ierr = MatNestCreateAggregateL2G_Private(A,vs->nc,vs->islocal.col,vs->isglobal.col,PETSC_TRUE,&cmap);CHKERRQ(ierr);
    if (rmap && cmap) {ierr = MatSetLocalToGlobalMapping(A,rmap,cmap);CHKERRQ(ierr);}
    ierr = ISLocalToGlobalMappingDestroy(&rmap);CHKERRQ(ierr);
    ierr = ISLocalToGlobalMappingDestroy(&cmap);CHKERRQ(ierr);
  }

#if defined(PETSC_USE_DEBUG)
  for (i=0; i<vs->nr; i++) {
    for (j=0; j<vs->nc; j++) {
      PetscInt m,n,M,N,mi,ni,Mi,Ni;
      Mat      B = vs->m[i][j];
      if (!B) continue;
      ierr = MatGetSize(B,&M,&N);CHKERRQ(ierr);
      ierr = MatGetLocalSize(B,&m,&n);CHKERRQ(ierr);
      ierr = ISGetSize(vs->isglobal.row[i],&Mi);CHKERRQ(ierr);
      ierr = ISGetSize(vs->isglobal.col[j],&Ni);CHKERRQ(ierr);
      ierr = ISGetLocalSize(vs->isglobal.row[i],&mi);CHKERRQ(ierr);
      ierr = ISGetLocalSize(vs->isglobal.col[j],&ni);CHKERRQ(ierr);
      if (M != Mi || N != Ni) SETERRQ6(PetscObjectComm((PetscObject)sub),PETSC_ERR_ARG_INCOMP,"Global sizes (%D,%D) of nested submatrix (%D,%D) do not agree with space defined by index sets (%D,%D)",M,N,i,j,Mi,Ni);
      if (m != mi || n != ni) SETERRQ6(PetscObjectComm((PetscObject)sub),PETSC_ERR_ARG_INCOMP,"Local sizes (%D,%D) of nested submatrix (%D,%D) do not agree with space defined by index sets (%D,%D)",m,n,i,j,mi,ni);
    }
  }
#endif

  /* Set A->assembled if all non-null blocks are currently assembled */
  for (i=0; i<vs->nr; i++) {
    for (j=0; j<vs->nc; j++) {
      if (vs->m[i][j] && !vs->m[i][j]->assembled) PetscFunctionReturn(0);
    }
  }
  A->assembled = PETSC_TRUE;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatCreateNest"
/*@C
   MatCreateNest - Creates a new matrix containing several nested submatrices, each stored separately

   Collective on Mat

   Input Parameter:
+  comm - Communicator for the new Mat
.  nr - number of nested row blocks
.  is_row - index sets for each nested row block, or NULL to make contiguous
.  nc - number of nested column blocks
.  is_col - index sets for each nested column block, or NULL to make contiguous
-  a - row-aligned array of nr*nc submatrices, empty submatrices can be passed using NULL

   Output Parameter:
.  B - new matrix

   Level: advanced

.seealso: MatCreate(), VecCreateNest(), DMCreateMatrix(), MATNEST
@*/
PetscErrorCode MatCreateNest(MPI_Comm comm,PetscInt nr,const IS is_row[],PetscInt nc,const IS is_col[],const Mat a[],Mat *B)
{
  Mat            A;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  *B   = 0;
  ierr = MatCreate(comm,&A);CHKERRQ(ierr);
  ierr = MatSetType(A,MATNEST);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);
  ierr = MatNestSetSubMats(A,nr,is_row,nc,is_col,a);CHKERRQ(ierr);
  *B   = A;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "MatConvert_Nest_AIJ"
PETSC_INTERN PetscErrorCode MatConvert_Nest_AIJ(Mat A,MatType newtype,MatReuse reuse,Mat *newmat)
{
  PetscErrorCode ierr;
  Mat_Nest       *nest = (Mat_Nest*)A->data;
  PetscInt       m,n,M,N,i,j,k,*dnnz,*onnz,rstart;
  PetscInt       cstart,cend;
  Mat            C;

  PetscFunctionBegin;
  ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr);
  ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
  ierr = MatGetOwnershipRangeColumn(A,&cstart,&cend);CHKERRQ(ierr);
  switch (reuse) {
  case MAT_INITIAL_MATRIX:
    ierr    = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr);
    ierr    = MatSetType(C,newtype);CHKERRQ(ierr);
    ierr    = MatSetSizes(C,m,n,M,N);CHKERRQ(ierr);
    *newmat = C;
    break;
  case MAT_REUSE_MATRIX:
    C = *newmat;
    break;
  default: SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"MatReuse");
  }
  ierr = PetscMalloc1(2*m,&dnnz);CHKERRQ(ierr);
  onnz = dnnz + m;
  for (k=0; k<m; k++) {
    dnnz[k] = 0;
    onnz[k] = 0;
  }
  for (j=0; j<nest->nc; ++j) {
    IS             bNis;
    PetscInt       bN;
    const PetscInt *bNindices;
    /* Using global column indices and ISAllGather() is not scalable. */
    ierr = ISAllGather(nest->isglobal.col[j], &bNis);CHKERRQ(ierr);
    ierr = ISGetSize(bNis, &bN);CHKERRQ(ierr);
    ierr = ISGetIndices(bNis,&bNindices);CHKERRQ(ierr);
    for (i=0; i<nest->nr; ++i) {
      PetscSF        bmsf;
      PetscSFNode    *iremote;
      Mat            B;
      PetscInt       bm, *sub_dnnz,*sub_onnz, br;
      const PetscInt *bmindices;
      B = nest->m[i][j];
      if (!B) continue;
      ierr = ISGetLocalSize(nest->isglobal.row[i],&bm);CHKERRQ(ierr);
      ierr = ISGetIndices(nest->isglobal.row[i],&bmindices);CHKERRQ(ierr);
      ierr = PetscSFCreate(PetscObjectComm((PetscObject)A), &bmsf);CHKERRQ(ierr);
      ierr = PetscMalloc1(bm,&iremote);CHKERRQ(ierr);
      ierr = PetscMalloc1(bm,&sub_dnnz);CHKERRQ(ierr);
      ierr = PetscMalloc1(bm,&sub_onnz);CHKERRQ(ierr);
      for (k = 0; k < bm; ++k){
    	sub_dnnz[k] = 0;
    	sub_onnz[k] = 0;
      }
      /*
       Locate the owners for all of the locally-owned global row indices for this row block.
       These determine the roots of PetscSF used to communicate preallocation data to row owners.
       The roots correspond to the dnnz and onnz entries; thus, there are two roots per row.
       */
      ierr = MatGetOwnershipRange(B,&rstart,NULL);CHKERRQ(ierr);
      for (br = 0; br < bm; ++br) {
        PetscInt       row = bmindices[br], rowowner = 0, brncols, col;
        const PetscInt *brcols;
        PetscInt       rowrel = 0; /* row's relative index on its owner rank */
        ierr      = PetscLayoutFindOwnerIndex(A->rmap,row,&rowowner,&rowrel);CHKERRQ(ierr);
        /* how many roots  */
        iremote[br].rank = rowowner; iremote[br].index = rowrel;           /* edge from bmdnnz to dnnz */
        /* get nonzero pattern */
        ierr = MatGetRow(B,br+rstart,&brncols,&brcols,NULL);CHKERRQ(ierr);
        for (k=0; k<brncols; k++) {
          col  = bNindices[brcols[k]];
          if(col>=A->cmap->range[rowowner] && col<A->cmap->range[rowowner+1]){
        	sub_dnnz[br]++;
          }else{
        	sub_onnz[br]++;
          }
        }
        ierr = MatRestoreRow(B,br+rstart,&brncols,&brcols,NULL);CHKERRQ(ierr);
      }
      ierr = ISRestoreIndices(nest->isglobal.row[i],&bmindices);CHKERRQ(ierr);
      /* bsf will have to take care of disposing of bedges. */
      ierr = PetscSFSetGraph(bmsf,m,bm,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr);
      ierr = PetscSFReduceBegin(bmsf,MPIU_INT,sub_dnnz,dnnz,MPI_SUM);CHKERRQ(ierr);
      ierr = PetscSFReduceEnd(bmsf,MPIU_INT,sub_dnnz,dnnz,MPI_SUM);CHKERRQ(ierr);
      ierr = PetscSFReduceBegin(bmsf,MPIU_INT,sub_onnz,onnz,MPI_SUM);CHKERRQ(ierr);
      ierr = PetscSFReduceEnd(bmsf,MPIU_INT,sub_onnz,onnz,MPI_SUM);CHKERRQ(ierr);
      ierr = PetscFree(sub_dnnz);CHKERRQ(ierr);
      ierr = PetscFree(sub_onnz);CHKERRQ(ierr);
      ierr = PetscSFDestroy(&bmsf);CHKERRQ(ierr);
    }
    ierr = ISRestoreIndices(bNis,&bNindices);CHKERRQ(ierr);
    ierr = ISDestroy(&bNis);CHKERRQ(ierr);
  }
  ierr = MatSeqAIJSetPreallocation(C,0,dnnz);CHKERRQ(ierr);
  ierr = MatMPIAIJSetPreallocation(C,0,dnnz,0,onnz);CHKERRQ(ierr);
  ierr = PetscFree(dnnz);CHKERRQ(ierr);

  /* Fill by row */
  for (j=0; j<nest->nc; ++j) {
    /* Using global column indices and ISAllGather() is not scalable. */
    IS             bNis;
    PetscInt       bN;
    const PetscInt *bNindices;
    ierr = ISAllGather(nest->isglobal.col[j], &bNis);CHKERRQ(ierr);
    ierr = ISGetSize(bNis,&bN);CHKERRQ(ierr);
    ierr = ISGetIndices(bNis,&bNindices);CHKERRQ(ierr);
    for (i=0; i<nest->nr; ++i) {
      Mat            B;
      PetscInt       bm, br;
      const PetscInt *bmindices;
      B = nest->m[i][j];
      if (!B) continue;
      ierr = ISGetLocalSize(nest->isglobal.row[i],&bm);CHKERRQ(ierr);
      ierr = ISGetIndices(nest->isglobal.row[i],&bmindices);CHKERRQ(ierr);
      ierr = MatGetOwnershipRange(B,&rstart,NULL);CHKERRQ(ierr);
      for (br = 0; br < bm; ++br) {
        PetscInt          row = bmindices[br], brncols,  *cols;
        const PetscInt    *brcols;
        const PetscScalar *brcoldata;
        ierr = MatGetRow(B,br+rstart,&brncols,&brcols,&brcoldata);CHKERRQ(ierr);
        ierr = PetscMalloc1(brncols,&cols);CHKERRQ(ierr);
        for (k=0; k<brncols; k++) cols[k] = bNindices[brcols[k]];
        /*
          Nest blocks are required to be nonoverlapping -- otherwise nest and monolithic index layouts wouldn't match.
          Thus, we could use INSERT_VALUES, but I prefer ADD_VALUES.
         */
        ierr = MatSetValues(C,1,&row,brncols,cols,brcoldata,ADD_VALUES);CHKERRQ(ierr);
        ierr = MatRestoreRow(B,br+rstart,&brncols,&brcols,&brcoldata);CHKERRQ(ierr);
        ierr = PetscFree(cols);CHKERRQ(ierr);
      }
      ierr = ISRestoreIndices(nest->isglobal.row[i],&bmindices);CHKERRQ(ierr);
    }
    ierr = ISRestoreIndices(bNis,&bNindices);CHKERRQ(ierr);
    ierr = ISDestroy(&bNis);CHKERRQ(ierr);
  }
  ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*MC
  MATNEST - MATNEST = "nest" - Matrix type consisting of nested submatrices, each stored separately.

  Level: intermediate

  Notes:
  This matrix type permits scalable use of PCFieldSplit and avoids the large memory costs of extracting submatrices.
  It allows the use of symmetric and block formats for parts of multi-physics simulations.
  It is usually used with DMComposite and DMCreateMatrix()

.seealso: MatCreate(), MatType, MatCreateNest()
M*/
#undef __FUNCT__
#define __FUNCT__ "MatCreate_Nest"
PETSC_EXTERN PetscErrorCode MatCreate_Nest(Mat A)
{
  Mat_Nest       *s;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr    = PetscNewLog(A,&s);CHKERRQ(ierr);
  A->data = (void*)s;

  s->nr            = -1;
  s->nc            = -1;
  s->m             = NULL;
  s->splitassembly = PETSC_FALSE;

  ierr = PetscMemzero(A->ops,sizeof(*A->ops));CHKERRQ(ierr);

  A->ops->mult                  = MatMult_Nest;
  A->ops->multadd               = MatMultAdd_Nest;
  A->ops->multtranspose         = MatMultTranspose_Nest;
  A->ops->multtransposeadd      = MatMultTransposeAdd_Nest;
  A->ops->assemblybegin         = MatAssemblyBegin_Nest;
  A->ops->assemblyend           = MatAssemblyEnd_Nest;
  A->ops->zeroentries           = MatZeroEntries_Nest;
  A->ops->copy                  = MatCopy_Nest;
  A->ops->duplicate             = MatDuplicate_Nest;
  A->ops->getsubmatrix          = MatGetSubMatrix_Nest;
  A->ops->destroy               = MatDestroy_Nest;
  A->ops->view                  = MatView_Nest;
  A->ops->getvecs               = 0; /* Use VECNEST by calling MatNestSetVecType(A,VECNEST) */
  A->ops->getlocalsubmatrix     = MatGetLocalSubMatrix_Nest;
  A->ops->restorelocalsubmatrix = MatRestoreLocalSubMatrix_Nest;
  A->ops->getdiagonal           = MatGetDiagonal_Nest;
  A->ops->diagonalscale         = MatDiagonalScale_Nest;
  A->ops->scale                 = MatScale_Nest;
  A->ops->shift                 = MatShift_Nest;

  A->spptr        = 0;
  A->assembled    = PETSC_FALSE;

  /* expose Nest api's */
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestGetSubMat_C",   MatNestGetSubMat_Nest);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestSetSubMat_C",   MatNestSetSubMat_Nest);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestGetSubMats_C",  MatNestGetSubMats_Nest);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestGetSize_C",     MatNestGetSize_Nest);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestGetISs_C",      MatNestGetISs_Nest);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestGetLocalISs_C", MatNestGetLocalISs_Nest);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestSetVecType_C",  MatNestSetVecType_Nest);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatNestSetSubMats_C",  MatNestSetSubMats_Nest);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_nest_aij_C",MatConvert_Nest_AIJ);CHKERRQ(ierr);

  ierr = PetscObjectChangeTypeName((PetscObject)A,MATNEST);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}