xref: /petsc/src/mat/impls/aij/mpi/mpiaij.c (revision 8d45306e634bbd2744ee6c3c0dbd500e7a33df16)

#include <../src/mat/impls/aij/mpi/mpiaij.h>   /*I "petscmat.h" I*/
#include <petsc/private/vecimpl.h>
#include <petsc/private/isimpl.h>
#include <petscblaslapack.h>
#include <petscsf.h>

/*MC
   MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices.

   This matrix type is identical to MATSEQAIJ when constructed with a single process communicator,
   and MATMPIAIJ otherwise.  As a result, for single process communicators,
  MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported
  for communicators controlling multiple processes.  It is recommended that you call both of
  the above preallocation routines for simplicity.

   Options Database Keys:
. -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions()

  Developer Notes: Subclasses include MATAIJCUSP, MATAIJCUSPARSE, MATAIJPERM, MATAIJCRL, and also automatically switches over to use inodes when
   enough exist.

  Level: beginner

.seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ, MATMPIAIJ
M*/

/*MC
   MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices.

   This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator,
   and MATMPIAIJCRL otherwise.  As a result, for single process communicators,
   MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported
  for communicators controlling multiple processes.  It is recommended that you call both of
  the above preallocation routines for simplicity.

   Options Database Keys:
. -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions()

  Level: beginner

.seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL
M*/

PetscErrorCode MatSetBlockSizes_MPIAIJ(Mat M, PetscInt rbs, PetscInt cbs)
{
  PetscErrorCode ierr;
  Mat_MPIAIJ     *mat = (Mat_MPIAIJ*)M->data;

  PetscFunctionBegin;
  if (mat->A) {
    ierr = MatSetBlockSizes(mat->A,rbs,cbs);CHKERRQ(ierr);
    ierr = MatSetBlockSizes(mat->B,rbs,1);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M,IS *keptrows)
{
  PetscErrorCode  ierr;
  Mat_MPIAIJ      *mat = (Mat_MPIAIJ*)M->data;
  Mat_SeqAIJ      *a   = (Mat_SeqAIJ*)mat->A->data;
  Mat_SeqAIJ      *b   = (Mat_SeqAIJ*)mat->B->data;
  const PetscInt  *ia,*ib;
  const MatScalar *aa,*bb;
  PetscInt        na,nb,i,j,*rows,cnt=0,n0rows;
  PetscInt        m = M->rmap->n,rstart = M->rmap->rstart;

  PetscFunctionBegin;
  *keptrows = 0;
  ia        = a->i;
  ib        = b->i;
  for (i=0; i<m; i++) {
    na = ia[i+1] - ia[i];
    nb = ib[i+1] - ib[i];
    if (!na && !nb) {
      cnt++;
      goto ok1;
    }
    aa = a->a + ia[i];
    for (j=0; j<na; j++) {
      if (aa[j] != 0.0) goto ok1;
    }
    bb = b->a + ib[i];
    for (j=0; j <nb; j++) {
      if (bb[j] != 0.0) goto ok1;
    }
    cnt++;
ok1:;
  }
  ierr = MPIU_Allreduce(&cnt,&n0rows,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)M));CHKERRQ(ierr);
  if (!n0rows) PetscFunctionReturn(0);
  ierr = PetscMalloc1(M->rmap->n-cnt,&rows);CHKERRQ(ierr);
  cnt  = 0;
  for (i=0; i<m; i++) {
    na = ia[i+1] - ia[i];
    nb = ib[i+1] - ib[i];
    if (!na && !nb) continue;
    aa = a->a + ia[i];
    for (j=0; j<na;j++) {
      if (aa[j] != 0.0) {
        rows[cnt++] = rstart + i;
        goto ok2;
      }
    }
    bb = b->a + ib[i];
    for (j=0; j<nb; j++) {
      if (bb[j] != 0.0) {
        rows[cnt++] = rstart + i;
        goto ok2;
      }
    }
ok2:;
  }
  ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode  MatDiagonalSet_MPIAIJ(Mat Y,Vec D,InsertMode is)
{
  PetscErrorCode    ierr;
  Mat_MPIAIJ        *aij = (Mat_MPIAIJ*) Y->data;

  PetscFunctionBegin;
  if (Y->assembled && Y->rmap->rstart == Y->cmap->rstart && Y->rmap->rend == Y->cmap->rend) {
    ierr = MatDiagonalSet(aij->A,D,is);CHKERRQ(ierr);
  } else {
    ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M,IS *zrows)
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)M->data;
  PetscErrorCode ierr;
  PetscInt       i,rstart,nrows,*rows;

  PetscFunctionBegin;
  *zrows = NULL;
  ierr   = MatFindZeroDiagonals_SeqAIJ_Private(aij->A,&nrows,&rows);CHKERRQ(ierr);
  ierr   = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr);
  for (i=0; i<nrows; i++) rows[i] += rstart;
  ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatGetColumnNorms_MPIAIJ(Mat A,NormType type,PetscReal *norms)
{
  PetscErrorCode ierr;
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)A->data;
  PetscInt       i,n,*garray = aij->garray;
  Mat_SeqAIJ     *a_aij = (Mat_SeqAIJ*) aij->A->data;
  Mat_SeqAIJ     *b_aij = (Mat_SeqAIJ*) aij->B->data;
  PetscReal      *work;

  PetscFunctionBegin;
  ierr = MatGetSize(A,NULL,&n);CHKERRQ(ierr);
  ierr = PetscCalloc1(n,&work);CHKERRQ(ierr);
  if (type == NORM_2) {
    for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) {
      work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]*a_aij->a[i]);
    }
    for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) {
      work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]*b_aij->a[i]);
    }
  } else if (type == NORM_1) {
    for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) {
      work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]);
    }
    for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) {
      work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]);
    }
  } else if (type == NORM_INFINITY) {
    for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) {
      work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]);
    }
    for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) {
      work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]),work[garray[b_aij->j[i]]]);
    }

  } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType");
  if (type == NORM_INFINITY) {
    ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr);
  } else {
    ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr);
  }
  ierr = PetscFree(work);CHKERRQ(ierr);
  if (type == NORM_2) {
    for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatFindOffBlockDiagonalEntries_MPIAIJ(Mat A,IS *is)
{
  Mat_MPIAIJ      *a  = (Mat_MPIAIJ*)A->data;
  IS              sis,gis;
  PetscErrorCode  ierr;
  const PetscInt  *isis,*igis;
  PetscInt        n,*iis,nsis,ngis,rstart,i;

  PetscFunctionBegin;
  ierr = MatFindOffBlockDiagonalEntries(a->A,&sis);CHKERRQ(ierr);
  ierr = MatFindNonzeroRows(a->B,&gis);CHKERRQ(ierr);
  ierr = ISGetSize(gis,&ngis);CHKERRQ(ierr);
  ierr = ISGetSize(sis,&nsis);CHKERRQ(ierr);
  ierr = ISGetIndices(sis,&isis);CHKERRQ(ierr);
  ierr = ISGetIndices(gis,&igis);CHKERRQ(ierr);

  ierr = PetscMalloc1(ngis+nsis,&iis);CHKERRQ(ierr);
  ierr = PetscMemcpy(iis,igis,ngis*sizeof(PetscInt));CHKERRQ(ierr);
  ierr = PetscMemcpy(iis+ngis,isis,nsis*sizeof(PetscInt));CHKERRQ(ierr);
  n    = ngis + nsis;
  ierr = PetscSortRemoveDupsInt(&n,iis);CHKERRQ(ierr);
  ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr);
  for (i=0; i<n; i++) iis[i] += rstart;
  ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),n,iis,PETSC_OWN_POINTER,is);CHKERRQ(ierr);

  ierr = ISRestoreIndices(sis,&isis);CHKERRQ(ierr);
  ierr = ISRestoreIndices(gis,&igis);CHKERRQ(ierr);
  ierr = ISDestroy(&sis);CHKERRQ(ierr);
  ierr = ISDestroy(&gis);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
    Distributes a SeqAIJ matrix across a set of processes. Code stolen from
    MatLoad_MPIAIJ(). Horrible lack of reuse. Should be a routine for each matrix type.

    Only for square matrices

    Used by a preconditioner, hence PETSC_EXTERN
*/
PETSC_EXTERN PetscErrorCode MatDistribute_MPIAIJ(MPI_Comm comm,Mat gmat,PetscInt m,MatReuse reuse,Mat *inmat)
{
  PetscMPIInt    rank,size;
  PetscInt       *rowners,*dlens,*olens,i,rstart,rend,j,jj,nz = 0,*gmataj,cnt,row,*ld,bses[2];
  PetscErrorCode ierr;
  Mat            mat;
  Mat_SeqAIJ     *gmata;
  PetscMPIInt    tag;
  MPI_Status     status;
  PetscBool      aij;
  MatScalar      *gmataa,*ao,*ad,*gmataarestore=0;

  PetscFunctionBegin;
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  if (!rank) {
    ierr = PetscObjectTypeCompare((PetscObject)gmat,MATSEQAIJ,&aij);CHKERRQ(ierr);
    if (!aij) SETERRQ1(PetscObjectComm((PetscObject)gmat),PETSC_ERR_SUP,"Currently no support for input matrix of type %s\n",((PetscObject)gmat)->type_name);
  }
  if (reuse == MAT_INITIAL_MATRIX) {
    ierr = MatCreate(comm,&mat);CHKERRQ(ierr);
    ierr = MatSetSizes(mat,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
    ierr = MatGetBlockSizes(gmat,&bses[0],&bses[1]);CHKERRQ(ierr);
    ierr = MPI_Bcast(bses,2,MPIU_INT,0,comm);CHKERRQ(ierr);
    ierr = MatSetBlockSizes(mat,bses[0],bses[1]);CHKERRQ(ierr);
    ierr = MatSetType(mat,MATAIJ);CHKERRQ(ierr);
    ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr);
    ierr = PetscMalloc2(m,&dlens,m,&olens);CHKERRQ(ierr);
    ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr);

    rowners[0] = 0;
    for (i=2; i<=size; i++) rowners[i] += rowners[i-1];
    rstart = rowners[rank];
    rend   = rowners[rank+1];
    ierr   = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr);
    if (!rank) {
      gmata = (Mat_SeqAIJ*) gmat->data;
      /* send row lengths to all processors */
      for (i=0; i<m; i++) dlens[i] = gmata->ilen[i];
      for (i=1; i<size; i++) {
        ierr = MPI_Send(gmata->ilen + rowners[i],rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr);
      }
      /* determine number diagonal and off-diagonal counts */
      ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr);
      ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr);
      jj   = 0;
      for (i=0; i<m; i++) {
        for (j=0; j<dlens[i]; j++) {
          if (gmata->j[jj] < rstart) ld[i]++;
          if (gmata->j[jj] < rstart || gmata->j[jj] >= rend) olens[i]++;
          jj++;
        }
      }
      /* send column indices to other processes */
      for (i=1; i<size; i++) {
        nz   = gmata->i[rowners[i+1]]-gmata->i[rowners[i]];
        ierr = MPI_Send(&nz,1,MPIU_INT,i,tag,comm);CHKERRQ(ierr);
        ierr = MPI_Send(gmata->j + gmata->i[rowners[i]],nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr);
      }

      /* send numerical values to other processes */
      for (i=1; i<size; i++) {
        nz   = gmata->i[rowners[i+1]]-gmata->i[rowners[i]];
        ierr = MPI_Send(gmata->a + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr);
      }
      gmataa = gmata->a;
      gmataj = gmata->j;

    } else {
      /* receive row lengths */
      ierr = MPI_Recv(dlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr);
      /* receive column indices */
      ierr = MPI_Recv(&nz,1,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr);
      ierr = PetscMalloc2(nz,&gmataa,nz,&gmataj);CHKERRQ(ierr);
      ierr = MPI_Recv(gmataj,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr);
      /* determine number diagonal and off-diagonal counts */
      ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr);
      ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr);
      jj   = 0;
      for (i=0; i<m; i++) {
        for (j=0; j<dlens[i]; j++) {
          if (gmataj[jj] < rstart) ld[i]++;
          if (gmataj[jj] < rstart || gmataj[jj] >= rend) olens[i]++;
          jj++;
        }
      }
      /* receive numerical values */
      ierr = PetscMemzero(gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr);
      ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr);
    }
    /* set preallocation */
    for (i=0; i<m; i++) {
      dlens[i] -= olens[i];
    }
    ierr = MatSeqAIJSetPreallocation(mat,0,dlens);CHKERRQ(ierr);
    ierr = MatMPIAIJSetPreallocation(mat,0,dlens,0,olens);CHKERRQ(ierr);

    for (i=0; i<m; i++) {
      dlens[i] += olens[i];
    }
    cnt = 0;
    for (i=0; i<m; i++) {
      row  = rstart + i;
      ierr = MatSetValues(mat,1,&row,dlens[i],gmataj+cnt,gmataa+cnt,INSERT_VALUES);CHKERRQ(ierr);
      cnt += dlens[i];
    }
    if (rank) {
      ierr = PetscFree2(gmataa,gmataj);CHKERRQ(ierr);
    }
    ierr = PetscFree2(dlens,olens);CHKERRQ(ierr);
    ierr = PetscFree(rowners);CHKERRQ(ierr);

    ((Mat_MPIAIJ*)(mat->data))->ld = ld;

    *inmat = mat;
  } else {   /* column indices are already set; only need to move over numerical values from process 0 */
    Mat_SeqAIJ *Ad = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->A->data;
    Mat_SeqAIJ *Ao = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->B->data;
    mat  = *inmat;
    ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr);
    if (!rank) {
      /* send numerical values to other processes */
      gmata  = (Mat_SeqAIJ*) gmat->data;
      ierr   = MatGetOwnershipRanges(mat,(const PetscInt**)&rowners);CHKERRQ(ierr);
      gmataa = gmata->a;
      for (i=1; i<size; i++) {
        nz   = gmata->i[rowners[i+1]]-gmata->i[rowners[i]];
        ierr = MPI_Send(gmataa + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr);
      }
      nz = gmata->i[rowners[1]]-gmata->i[rowners[0]];
    } else {
      /* receive numerical values from process 0*/
      nz   = Ad->nz + Ao->nz;
      ierr = PetscMalloc1(nz,&gmataa);CHKERRQ(ierr); gmataarestore = gmataa;
      ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr);
    }
    /* transfer numerical values into the diagonal A and off diagonal B parts of mat */
    ld = ((Mat_MPIAIJ*)(mat->data))->ld;
    ad = Ad->a;
    ao = Ao->a;
    if (mat->rmap->n) {
      i  = 0;
      nz = ld[i];                                   ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz;
      nz = Ad->i[i+1] - Ad->i[i];                   ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz;
    }
    for (i=1; i<mat->rmap->n; i++) {
      nz = Ao->i[i] - Ao->i[i-1] - ld[i-1] + ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz;
      nz = Ad->i[i+1] - Ad->i[i];                   ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz;
    }
    i--;
    if (mat->rmap->n) {
      nz = Ao->i[i+1] - Ao->i[i] - ld[i];           ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr);
    }
    if (rank) {
      ierr = PetscFree(gmataarestore);CHKERRQ(ierr);
    }
  }
  ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
  Local utility routine that creates a mapping from the global column
number to the local number in the off-diagonal part of the local
storage of the matrix.  When PETSC_USE_CTABLE is used this is scalable at
a slightly higher hash table cost; without it it is not scalable (each processor
has an order N integer array but is fast to acess.
*/
PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat)
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  PetscErrorCode ierr;
  PetscInt       n = aij->B->cmap->n,i;

  PetscFunctionBegin;
  if (!aij->garray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPIAIJ Matrix was assembled but is missing garray");
#if defined(PETSC_USE_CTABLE)
  ierr = PetscTableCreate(n,mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr);
  for (i=0; i<n; i++) {
    ierr = PetscTableAdd(aij->colmap,aij->garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr);
  }
#else
  ierr = PetscCalloc1(mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr);
  ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N+1)*sizeof(PetscInt));CHKERRQ(ierr);
  for (i=0; i<n; i++) aij->colmap[aij->garray[i]] = i+1;
#endif
  PetscFunctionReturn(0);
}

#define MatSetValues_SeqAIJ_A_Private(row,col,value,addv,orow,ocol)     \
{ \
    if (col <= lastcol1)  low1 = 0;     \
    else                 high1 = nrow1; \
    lastcol1 = col;\
    while (high1-low1 > 5) { \
      t = (low1+high1)/2; \
      if (rp1[t] > col) high1 = t; \
      else              low1  = t; \
    } \
      for (_i=low1; _i<high1; _i++) { \
        if (rp1[_i] > col) break; \
        if (rp1[_i] == col) { \
          if (addv == ADD_VALUES) ap1[_i] += value;   \
          else                    ap1[_i] = value; \
          goto a_noinsert; \
        } \
      }  \
      if (value == 0.0 && ignorezeroentries && row != col) {low1 = 0; high1 = nrow1;goto a_noinsert;} \
      if (nonew == 1) {low1 = 0; high1 = nrow1; goto a_noinsert;}                \
      if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \
      MatSeqXAIJReallocateAIJ(A,am,1,nrow1,row,col,rmax1,aa,ai,aj,rp1,ap1,aimax,nonew,MatScalar); \
      N = nrow1++ - 1; a->nz++; high1++; \
      /* shift up all the later entries in this row */ \
      for (ii=N; ii>=_i; ii--) { \
        rp1[ii+1] = rp1[ii]; \
        ap1[ii+1] = ap1[ii]; \
      } \
      rp1[_i] = col;  \
      ap1[_i] = value;  \
      A->nonzerostate++;\
      a_noinsert: ; \
      ailen[row] = nrow1; \
}

#define MatSetValues_SeqAIJ_B_Private(row,col,value,addv,orow,ocol) \
  { \
    if (col <= lastcol2) low2 = 0;                        \
    else high2 = nrow2;                                   \
    lastcol2 = col;                                       \
    while (high2-low2 > 5) {                              \
      t = (low2+high2)/2;                                 \
      if (rp2[t] > col) high2 = t;                        \
      else             low2  = t;                         \
    }                                                     \
    for (_i=low2; _i<high2; _i++) {                       \
      if (rp2[_i] > col) break;                           \
      if (rp2[_i] == col) {                               \
        if (addv == ADD_VALUES) ap2[_i] += value;         \
        else                    ap2[_i] = value;          \
        goto b_noinsert;                                  \
      }                                                   \
    }                                                     \
    if (value == 0.0 && ignorezeroentries) {low2 = 0; high2 = nrow2; goto b_noinsert;} \
    if (nonew == 1) {low2 = 0; high2 = nrow2; goto b_noinsert;}                        \
    if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \
    MatSeqXAIJReallocateAIJ(B,bm,1,nrow2,row,col,rmax2,ba,bi,bj,rp2,ap2,bimax,nonew,MatScalar); \
    N = nrow2++ - 1; b->nz++; high2++;                    \
    /* shift up all the later entries in this row */      \
    for (ii=N; ii>=_i; ii--) {                            \
      rp2[ii+1] = rp2[ii];                                \
      ap2[ii+1] = ap2[ii];                                \
    }                                                     \
    rp2[_i] = col;                                        \
    ap2[_i] = value;                                      \
    B->nonzerostate++;                                    \
    b_noinsert: ;                                         \
    bilen[row] = nrow2;                                   \
  }

PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A,PetscInt row,const PetscScalar v[])
{
  Mat_MPIAIJ     *mat = (Mat_MPIAIJ*)A->data;
  Mat_SeqAIJ     *a   = (Mat_SeqAIJ*)mat->A->data,*b = (Mat_SeqAIJ*)mat->B->data;
  PetscErrorCode ierr;
  PetscInt       l,*garray = mat->garray,diag;

  PetscFunctionBegin;
  /* code only works for square matrices A */

  /* find size of row to the left of the diagonal part */
  ierr = MatGetOwnershipRange(A,&diag,0);CHKERRQ(ierr);
  row  = row - diag;
  for (l=0; l<b->i[row+1]-b->i[row]; l++) {
    if (garray[b->j[b->i[row]+l]] > diag) break;
  }
  ierr = PetscMemcpy(b->a+b->i[row],v,l*sizeof(PetscScalar));CHKERRQ(ierr);

  /* diagonal part */
  ierr = PetscMemcpy(a->a+a->i[row],v+l,(a->i[row+1]-a->i[row])*sizeof(PetscScalar));CHKERRQ(ierr);

  /* right of diagonal part */
  ierr = PetscMemcpy(b->a+b->i[row]+l,v+l+a->i[row+1]-a->i[row],(b->i[row+1]-b->i[row]-l)*sizeof(PetscScalar));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatSetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv)
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  PetscScalar    value;
  PetscErrorCode ierr;
  PetscInt       i,j,rstart  = mat->rmap->rstart,rend = mat->rmap->rend;
  PetscInt       cstart      = mat->cmap->rstart,cend = mat->cmap->rend,row,col;
  PetscBool      roworiented = aij->roworiented;

  /* Some Variables required in the macro */
  Mat        A                 = aij->A;
  Mat_SeqAIJ *a                = (Mat_SeqAIJ*)A->data;
  PetscInt   *aimax            = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j;
  MatScalar  *aa               = a->a;
  PetscBool  ignorezeroentries = a->ignorezeroentries;
  Mat        B                 = aij->B;
  Mat_SeqAIJ *b                = (Mat_SeqAIJ*)B->data;
  PetscInt   *bimax            = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n;
  MatScalar  *ba               = b->a;

  PetscInt  *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2;
  PetscInt  nonew;
  MatScalar *ap1,*ap2;

  PetscFunctionBegin;
  for (i=0; i<m; i++) {
    if (im[i] < 0) continue;
#if defined(PETSC_USE_DEBUG)
    if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1);
#endif
    if (im[i] >= rstart && im[i] < rend) {
      row      = im[i] - rstart;
      lastcol1 = -1;
      rp1      = aj + ai[row];
      ap1      = aa + ai[row];
      rmax1    = aimax[row];
      nrow1    = ailen[row];
      low1     = 0;
      high1    = nrow1;
      lastcol2 = -1;
      rp2      = bj + bi[row];
      ap2      = ba + bi[row];
      rmax2    = bimax[row];
      nrow2    = bilen[row];
      low2     = 0;
      high2    = nrow2;

      for (j=0; j<n; j++) {
        if (roworiented) value = v[i*n+j];
        else             value = v[i+j*m];
        if (in[j] >= cstart && in[j] < cend) {
          col   = in[j] - cstart;
          nonew = a->nonew;
          if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue;
          MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]);
        } else if (in[j] < 0) continue;
#if defined(PETSC_USE_DEBUG)
        else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1);
#endif
        else {
          if (mat->was_assembled) {
            if (!aij->colmap) {
              ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr);
            }
#if defined(PETSC_USE_CTABLE)
            ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr);
            col--;
#else
            col = aij->colmap[in[j]] - 1;
#endif
            if (col < 0 && !((Mat_SeqAIJ*)(aij->B->data))->nonew) {
              ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr);
              col  =  in[j];
              /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */
              B     = aij->B;
              b     = (Mat_SeqAIJ*)B->data;
              bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; ba = b->a;
              rp2   = bj + bi[row];
              ap2   = ba + bi[row];
              rmax2 = bimax[row];
              nrow2 = bilen[row];
              low2  = 0;
              high2 = nrow2;
              bm    = aij->B->rmap->n;
              ba    = b->a;
            } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", im[i], in[j]);
          } else col = in[j];
          nonew = b->nonew;
          MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]);
        }
      }
    } else {
      if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]);
      if (!aij->donotstash) {
        mat->assembled = PETSC_FALSE;
        if (roworiented) {
          ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr);
        } else {
          ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr);
        }
      }
    }
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatGetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[])
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  PetscErrorCode ierr;
  PetscInt       i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend;
  PetscInt       cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col;

  PetscFunctionBegin;
  for (i=0; i<m; i++) {
    if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/
    if (idxm[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm[i],mat->rmap->N-1);
    if (idxm[i] >= rstart && idxm[i] < rend) {
      row = idxm[i] - rstart;
      for (j=0; j<n; j++) {
        if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */
        if (idxn[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",idxn[j],mat->cmap->N-1);
        if (idxn[j] >= cstart && idxn[j] < cend) {
          col  = idxn[j] - cstart;
          ierr = MatGetValues(aij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr);
        } else {
          if (!aij->colmap) {
            ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr);
          }
#if defined(PETSC_USE_CTABLE)
          ierr = PetscTableFind(aij->colmap,idxn[j]+1,&col);CHKERRQ(ierr);
          col--;
#else
          col = aij->colmap[idxn[j]] - 1;
#endif
          if ((col < 0) || (aij->garray[col] != idxn[j])) *(v+i*n+j) = 0.0;
          else {
            ierr = MatGetValues(aij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr);
          }
        }
      }
    } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported");
  }
  PetscFunctionReturn(0);
}

extern PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat,Vec,Vec);

PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat,MatAssemblyType mode)
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  PetscErrorCode ierr;
  PetscInt       nstash,reallocs;

  PetscFunctionBegin;
  if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0);

  ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr);
  ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr);
  ierr = PetscInfo2(aij->A,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat,MatAssemblyType mode)
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  Mat_SeqAIJ     *a   = (Mat_SeqAIJ*)aij->A->data;
  PetscErrorCode ierr;
  PetscMPIInt    n;
  PetscInt       i,j,rstart,ncols,flg;
  PetscInt       *row,*col;
  PetscBool      other_disassembled;
  PetscScalar    *val;

  /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */

  PetscFunctionBegin;
  if (!aij->donotstash && !mat->nooffprocentries) {
    while (1) {
      ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr);
      if (!flg) break;

      for (i=0; i<n; ) {
        /* Now identify the consecutive vals belonging to the same row */
        for (j=i,rstart=row[j]; j<n; j++) {
          if (row[j] != rstart) break;
        }
        if (j < n) ncols = j-i;
        else       ncols = n-i;
        /* Now assemble all these values with a single function call */
        ierr = MatSetValues_MPIAIJ(mat,1,row+i,ncols,col+i,val+i,mat->insertmode);CHKERRQ(ierr);

        i = j;
      }
    }
    ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr);
  }
  ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(aij->A,mode);CHKERRQ(ierr);

  /* determine if any processor has disassembled, if so we must
     also disassemble ourselfs, in order that we may reassemble. */
  /*
     if nonzero structure of submatrix B cannot change then we know that
     no processor disassembled thus we can skip this stuff
  */
  if (!((Mat_SeqAIJ*)aij->B->data)->nonew) {
    ierr = MPIU_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
    if (mat->was_assembled && !other_disassembled) {
      ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr);
    }
  }
  if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) {
    ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr);
  }
  ierr = MatSetOption(aij->B,MAT_USE_INODES,PETSC_FALSE);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(aij->B,mode);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(aij->B,mode);CHKERRQ(ierr);

  ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr);

  aij->rowvalues = 0;

  ierr = VecDestroy(&aij->diag);CHKERRQ(ierr);
  if (a->inode.size) mat->ops->multdiagonalblock = MatMultDiagonalBlock_MPIAIJ;

  /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */
  if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqAIJ*)(aij->A->data))->nonew) {
    PetscObjectState state = aij->A->nonzerostate + aij->B->nonzerostate;
    ierr = MPIU_Allreduce(&state,&mat->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatZeroEntries_MPIAIJ(Mat A)
{
  Mat_MPIAIJ     *l = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MatZeroEntries(l->A);CHKERRQ(ierr);
  ierr = MatZeroEntries(l->B);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatZeroRows_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b)
{
  Mat_MPIAIJ    *mat    = (Mat_MPIAIJ *) A->data;
  PetscInt      *lrows;
  PetscInt       r, len;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  /* get locally owned rows */
  ierr = MatZeroRowsMapLocal_Private(A,N,rows,&len,&lrows);CHKERRQ(ierr);
  /* fix right hand side if needed */
  if (x && b) {
    const PetscScalar *xx;
    PetscScalar       *bb;

    ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr);
    ierr = VecGetArray(b, &bb);CHKERRQ(ierr);
    for (r = 0; r < len; ++r) bb[lrows[r]] = diag*xx[lrows[r]];
    ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr);
    ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr);
  }
  /* Must zero l->B before l->A because the (diag) case below may put values into l->B*/
  ierr = MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr);
  if (A->congruentlayouts == -1) { /* first time we compare rows and cols layouts */
    PetscBool cong;
    ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr);
    if (cong) A->congruentlayouts = 1;
    else      A->congruentlayouts = 0;
  }
  if ((diag != 0.0) && A->congruentlayouts) {
    ierr = MatZeroRows(mat->A, len, lrows, diag, NULL, NULL);CHKERRQ(ierr);
  } else if (diag != 0.0) {
    ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr);
    if (((Mat_SeqAIJ *) mat->A->data)->nonew) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "MatZeroRows() on rectangular matrices cannot be used with the Mat options\nMAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR");
    for (r = 0; r < len; ++r) {
      const PetscInt row = lrows[r] + A->rmap->rstart;
      ierr = MatSetValues(A, 1, &row, 1, &row, &diag, INSERT_VALUES);CHKERRQ(ierr);
    }
    ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  } else {
    ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr);
  }
  ierr = PetscFree(lrows);CHKERRQ(ierr);

  /* only change matrix nonzero state if pattern was allowed to be changed */
  if (!((Mat_SeqAIJ*)(mat->A->data))->keepnonzeropattern) {
    PetscObjectState state = mat->A->nonzerostate + mat->B->nonzerostate;
    ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b)
{
  Mat_MPIAIJ        *l = (Mat_MPIAIJ*)A->data;
  PetscErrorCode    ierr;
  PetscMPIInt       n = A->rmap->n;
  PetscInt          i,j,r,m,p = 0,len = 0;
  PetscInt          *lrows,*owners = A->rmap->range;
  PetscSFNode       *rrows;
  PetscSF           sf;
  const PetscScalar *xx;
  PetscScalar       *bb,*mask;
  Vec               xmask,lmask;
  Mat_SeqAIJ        *aij = (Mat_SeqAIJ*)l->B->data;
  const PetscInt    *aj, *ii,*ridx;
  PetscScalar       *aa;

  PetscFunctionBegin;
  /* Create SF where leaves are input rows and roots are owned rows */
  ierr = PetscMalloc1(n, &lrows);CHKERRQ(ierr);
  for (r = 0; r < n; ++r) lrows[r] = -1;
  ierr = PetscMalloc1(N, &rrows);CHKERRQ(ierr);
  for (r = 0; r < N; ++r) {
    const PetscInt idx   = rows[r];
    if (idx < 0 || A->rmap->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range [0,%D)",idx,A->rmap->N);
    if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this row too */
      ierr = PetscLayoutFindOwner(A->rmap,idx,&p);CHKERRQ(ierr);
    }
    rrows[r].rank  = p;
    rrows[r].index = rows[r] - owners[p];
  }
  ierr = PetscSFCreate(PetscObjectComm((PetscObject) A), &sf);CHKERRQ(ierr);
  ierr = PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER);CHKERRQ(ierr);
  /* Collect flags for rows to be zeroed */
  ierr = PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr);
  ierr = PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&sf);CHKERRQ(ierr);
  /* Compress and put in row numbers */
  for (r = 0; r < n; ++r) if (lrows[r] >= 0) lrows[len++] = r;
  /* zero diagonal part of matrix */
  ierr = MatZeroRowsColumns(l->A,len,lrows,diag,x,b);CHKERRQ(ierr);
  /* handle off diagonal part of matrix */
  ierr = MatCreateVecs(A,&xmask,NULL);CHKERRQ(ierr);
  ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr);
  ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr);
  for (i=0; i<len; i++) bb[lrows[i]] = 1;
  ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr);
  ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecDestroy(&xmask);CHKERRQ(ierr);
  if (x) {
    ierr = VecScatterBegin(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = VecScatterEnd(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr);
    ierr = VecGetArray(b,&bb);CHKERRQ(ierr);
  }
  ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr);
  /* remove zeroed rows of off diagonal matrix */
  ii = aij->i;
  for (i=0; i<len; i++) {
    ierr = PetscMemzero(aij->a + ii[lrows[i]],(ii[lrows[i]+1] - ii[lrows[i]])*sizeof(PetscScalar));CHKERRQ(ierr);
  }
  /* loop over all elements of off process part of matrix zeroing removed columns*/
  if (aij->compressedrow.use) {
    m    = aij->compressedrow.nrows;
    ii   = aij->compressedrow.i;
    ridx = aij->compressedrow.rindex;
    for (i=0; i<m; i++) {
      n  = ii[i+1] - ii[i];
      aj = aij->j + ii[i];
      aa = aij->a + ii[i];

      for (j=0; j<n; j++) {
        if (PetscAbsScalar(mask[*aj])) {
          if (b) bb[*ridx] -= *aa*xx[*aj];
          *aa = 0.0;
        }
        aa++;
        aj++;
      }
      ridx++;
    }
  } else { /* do not use compressed row format */
    m = l->B->rmap->n;
    for (i=0; i<m; i++) {
      n  = ii[i+1] - ii[i];
      aj = aij->j + ii[i];
      aa = aij->a + ii[i];
      for (j=0; j<n; j++) {
        if (PetscAbsScalar(mask[*aj])) {
          if (b) bb[i] -= *aa*xx[*aj];
          *aa = 0.0;
        }
        aa++;
        aj++;
      }
    }
  }
  if (x) {
    ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr);
    ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr);
  }
  ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr);
  ierr = VecDestroy(&lmask);CHKERRQ(ierr);
  ierr = PetscFree(lrows);CHKERRQ(ierr);

  /* only change matrix nonzero state if pattern was allowed to be changed */
  if (!((Mat_SeqAIJ*)(l->A->data))->keepnonzeropattern) {
    PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate;
    ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatMult_MPIAIJ(Mat A,Vec xx,Vec yy)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;
  PetscInt       nt;

  PetscFunctionBegin;
  ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr);
  if (nt != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A (%D) and xx (%D)",A->cmap->n,nt);
  ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr);
  ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A,Vec bb,Vec xx)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MatMultDiagonalBlock(a->A,bb,xx);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatMultAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr);
  ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatMultTranspose_MPIAIJ(Mat A,Vec xx,Vec yy)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;
  PetscBool      merged;

  PetscFunctionBegin;
  ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr);
  /* do nondiagonal part */
  ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr);
  if (!merged) {
    /* send it on its way */
    ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
    /* do local part */
    ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr);
    /* receive remote parts: note this assumes the values are not actually */
    /* added in yy until the next line, */
    ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
  } else {
    /* do local part */
    ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr);
    /* send it on its way */
    ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
    /* values actually were received in the Begin() but we need to call this nop */
    ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat,Mat Bmat,PetscReal tol,PetscBool  *f)
{
  MPI_Comm       comm;
  Mat_MPIAIJ     *Aij = (Mat_MPIAIJ*) Amat->data, *Bij;
  Mat            Adia = Aij->A, Bdia, Aoff,Boff,*Aoffs,*Boffs;
  IS             Me,Notme;
  PetscErrorCode ierr;
  PetscInt       M,N,first,last,*notme,i;
  PetscMPIInt    size;

  PetscFunctionBegin;
  /* Easy test: symmetric diagonal block */
  Bij  = (Mat_MPIAIJ*) Bmat->data; Bdia = Bij->A;
  ierr = MatIsTranspose(Adia,Bdia,tol,f);CHKERRQ(ierr);
  if (!*f) PetscFunctionReturn(0);
  ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  if (size == 1) PetscFunctionReturn(0);

  /* Hard test: off-diagonal block. This takes a MatCreateSubMatrix. */
  ierr = MatGetSize(Amat,&M,&N);CHKERRQ(ierr);
  ierr = MatGetOwnershipRange(Amat,&first,&last);CHKERRQ(ierr);
  ierr = PetscMalloc1(N-last+first,&notme);CHKERRQ(ierr);
  for (i=0; i<first; i++) notme[i] = i;
  for (i=last; i<M; i++) notme[i-last+first] = i;
  ierr = ISCreateGeneral(MPI_COMM_SELF,N-last+first,notme,PETSC_COPY_VALUES,&Notme);CHKERRQ(ierr);
  ierr = ISCreateStride(MPI_COMM_SELF,last-first,first,1,&Me);CHKERRQ(ierr);
  ierr = MatCreateSubMatrices(Amat,1,&Me,&Notme,MAT_INITIAL_MATRIX,&Aoffs);CHKERRQ(ierr);
  Aoff = Aoffs[0];
  ierr = MatCreateSubMatrices(Bmat,1,&Notme,&Me,MAT_INITIAL_MATRIX,&Boffs);CHKERRQ(ierr);
  Boff = Boffs[0];
  ierr = MatIsTranspose(Aoff,Boff,tol,f);CHKERRQ(ierr);
  ierr = MatDestroyMatrices(1,&Aoffs);CHKERRQ(ierr);
  ierr = MatDestroyMatrices(1,&Boffs);CHKERRQ(ierr);
  ierr = ISDestroy(&Me);CHKERRQ(ierr);
  ierr = ISDestroy(&Notme);CHKERRQ(ierr);
  ierr = PetscFree(notme);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  /* do nondiagonal part */
  ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr);
  /* send it on its way */
  ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
  /* do local part */
  ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr);
  /* receive remote parts */
  ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
  This only works correctly for square matrices where the subblock A->A is the
   diagonal block
*/
PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A,Vec v)
{
  PetscErrorCode ierr;
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;

  PetscFunctionBegin;
  if (A->rmap->N != A->cmap->N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block");
  if (A->rmap->rstart != A->cmap->rstart || A->rmap->rend != A->cmap->rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"row partition must equal col partition");
  ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatScale_MPIAIJ(Mat A,PetscScalar aa)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MatScale(a->A,aa);CHKERRQ(ierr);
  ierr = MatScale(a->B,aa);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatDestroy_MPIAIJ(Mat mat)
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
#if defined(PETSC_USE_LOG)
  PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D",mat->rmap->N,mat->cmap->N);
#endif
  ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr);
  ierr = VecDestroy(&aij->diag);CHKERRQ(ierr);
  ierr = MatDestroy(&aij->A);CHKERRQ(ierr);
  ierr = MatDestroy(&aij->B);CHKERRQ(ierr);
#if defined(PETSC_USE_CTABLE)
  ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr);
#else
  ierr = PetscFree(aij->colmap);CHKERRQ(ierr);
#endif
  ierr = PetscFree(aij->garray);CHKERRQ(ierr);
  ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr);
  ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr);
  ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr);
  ierr = PetscFree(aij->ld);CHKERRQ(ierr);
  ierr = PetscFree(mat->data);CHKERRQ(ierr);

  ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)mat,"MatIsTranspose_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocation_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_mpisbaij_C",NULL);CHKERRQ(ierr);
#if defined(PETSC_HAVE_ELEMENTAL)
  ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_elemental_C",NULL);CHKERRQ(ierr);
#endif
#if defined(PETSC_HAVE_HYPRE)
  ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_hypre_C",NULL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMatMatMult_transpose_mpiaij_mpiaij_C",NULL);CHKERRQ(ierr);
#endif
  PetscFunctionReturn(0);
}

PetscErrorCode MatView_MPIAIJ_Binary(Mat mat,PetscViewer viewer)
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  Mat_SeqAIJ     *A   = (Mat_SeqAIJ*)aij->A->data;
  Mat_SeqAIJ     *B   = (Mat_SeqAIJ*)aij->B->data;
  PetscErrorCode ierr;
  PetscMPIInt    rank,size,tag = ((PetscObject)viewer)->tag;
  int            fd;
  PetscInt       nz,header[4],*row_lengths,*range=0,rlen,i;
  PetscInt       nzmax,*column_indices,j,k,col,*garray = aij->garray,cnt,cstart = mat->cmap->rstart,rnz = 0;
  PetscScalar    *column_values;
  PetscInt       message_count,flowcontrolcount;
  FILE           *file;

  PetscFunctionBegin;
  ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr);
  nz   = A->nz + B->nz;
  ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr);
  if (!rank) {
    header[0] = MAT_FILE_CLASSID;
    header[1] = mat->rmap->N;
    header[2] = mat->cmap->N;

    ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
    ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr);
    /* get largest number of rows any processor has */
    rlen  = mat->rmap->n;
    range = mat->rmap->range;
    for (i=1; i<size; i++) rlen = PetscMax(rlen,range[i+1] - range[i]);
  } else {
    ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
    rlen = mat->rmap->n;
  }

  /* load up the local row counts */
  ierr = PetscMalloc1(rlen+1,&row_lengths);CHKERRQ(ierr);
  for (i=0; i<mat->rmap->n; i++) row_lengths[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i];

  /* store the row lengths to the file */
  ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr);
  if (!rank) {
    ierr = PetscBinaryWrite(fd,row_lengths,mat->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr);
    for (i=1; i<size; i++) {
      ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr);
      rlen = range[i+1] - range[i];
      ierr = MPIULong_Recv(row_lengths,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
      ierr = PetscBinaryWrite(fd,row_lengths,rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr);
    }
    ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr);
  } else {
    ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr);
    ierr = MPIULong_Send(row_lengths,mat->rmap->n,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
    ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr);
  }
  ierr = PetscFree(row_lengths);CHKERRQ(ierr);

  /* load up the local column indices */
  nzmax = nz; /* th processor needs space a largest processor needs */
  ierr  = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
  ierr  = PetscMalloc1(nzmax+1,&column_indices);CHKERRQ(ierr);
  cnt   = 0;
  for (i=0; i<mat->rmap->n; i++) {
    for (j=B->i[i]; j<B->i[i+1]; j++) {
      if ((col = garray[B->j[j]]) > cstart) break;
      column_indices[cnt++] = col;
    }
    for (k=A->i[i]; k<A->i[i+1]; k++) column_indices[cnt++] = A->j[k] + cstart;
    for (; j<B->i[i+1]; j++) column_indices[cnt++] = garray[B->j[j]];
  }
  if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz);

  /* store the column indices to the file */
  ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr);
  if (!rank) {
    MPI_Status status;
    ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr);
    for (i=1; i<size; i++) {
      ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr);
      ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr);
      if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax);
      ierr = MPIULong_Recv(column_indices,rnz,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
      ierr = PetscBinaryWrite(fd,column_indices,rnz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr);
    }
    ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr);
  } else {
    ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr);
    ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
    ierr = MPIULong_Send(column_indices,nz,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
    ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr);
  }
  ierr = PetscFree(column_indices);CHKERRQ(ierr);

  /* load up the local column values */
  ierr = PetscMalloc1(nzmax+1,&column_values);CHKERRQ(ierr);
  cnt  = 0;
  for (i=0; i<mat->rmap->n; i++) {
    for (j=B->i[i]; j<B->i[i+1]; j++) {
      if (garray[B->j[j]] > cstart) break;
      column_values[cnt++] = B->a[j];
    }
    for (k=A->i[i]; k<A->i[i+1]; k++) column_values[cnt++] = A->a[k];
    for (; j<B->i[i+1]; j++) column_values[cnt++] = B->a[j];
  }
  if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz);

  /* store the column values to the file */
  ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr);
  if (!rank) {
    MPI_Status status;
    ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr);
    for (i=1; i<size; i++) {
      ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr);
      ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr);
      if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax);
      ierr = MPIULong_Recv(column_values,rnz,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
      ierr = PetscBinaryWrite(fd,column_values,rnz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr);
    }
    ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr);
  } else {
    ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr);
    ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
    ierr = MPIULong_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
    ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr);
  }
  ierr = PetscFree(column_values);CHKERRQ(ierr);

  ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr);
  if (file) fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(mat->rmap->bs));
  PetscFunctionReturn(0);
}

#include <petscdraw.h>
PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer)
{
  Mat_MPIAIJ        *aij = (Mat_MPIAIJ*)mat->data;
  PetscErrorCode    ierr;
  PetscMPIInt       rank = aij->rank,size = aij->size;
  PetscBool         isdraw,iascii,isbinary;
  PetscViewer       sviewer;
  PetscViewerFormat format;

  PetscFunctionBegin;
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr);
  if (iascii) {
    ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr);
    if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
      MatInfo   info;
      PetscBool inodes;

      ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr);
      ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr);
      ierr = MatInodeGetInodeSizes(aij->A,NULL,(PetscInt**)&inodes,NULL);CHKERRQ(ierr);
      ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr);
      if (!inodes) {
        ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, not using I-node routines\n",
                                                  rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr);
      } else {
        ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, using I-node routines\n",
                                                  rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr);
      }
      ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr);
      ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr);
      ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr);
      ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr);
      ierr = PetscViewerFlush(viewer);CHKERRQ(ierr);
      ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr);
      ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr);
      ierr = VecScatterView(aij->Mvctx,viewer);CHKERRQ(ierr);
      PetscFunctionReturn(0);
    } else if (format == PETSC_VIEWER_ASCII_INFO) {
      PetscInt inodecount,inodelimit,*inodes;
      ierr = MatInodeGetInodeSizes(aij->A,&inodecount,&inodes,&inodelimit);CHKERRQ(ierr);
      if (inodes) {
        ierr = PetscViewerASCIIPrintf(viewer,"using I-node (on process 0) routines: found %D nodes, limit used is %D\n",inodecount,inodelimit);CHKERRQ(ierr);
      } else {
        ierr = PetscViewerASCIIPrintf(viewer,"not using I-node (on process 0) routines\n");CHKERRQ(ierr);
      }
      PetscFunctionReturn(0);
    } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) {
      PetscFunctionReturn(0);
    }
  } else if (isbinary) {
    if (size == 1) {
      ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr);
      ierr = MatView(aij->A,viewer);CHKERRQ(ierr);
    } else {
      ierr = MatView_MPIAIJ_Binary(mat,viewer);CHKERRQ(ierr);
    }
    PetscFunctionReturn(0);
  } else if (isdraw) {
    PetscDraw draw;
    PetscBool isnull;
    ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
    ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr);
    if (isnull) PetscFunctionReturn(0);
  }

  {
    /* assemble the entire matrix onto first processor. */
    Mat        A;
    Mat_SeqAIJ *Aloc;
    PetscInt   M = mat->rmap->N,N = mat->cmap->N,m,*ai,*aj,row,*cols,i,*ct;
    MatScalar  *a;

    ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr);
    if (!rank) {
      ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr);
    } else {
      ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr);
    }
    /* This is just a temporary matrix, so explicitly using MATMPIAIJ is probably best */
    ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr);
    ierr = MatMPIAIJSetPreallocation(A,0,NULL,0,NULL);CHKERRQ(ierr);
    ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
    ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr);

    /* copy over the A part */
    Aloc = (Mat_SeqAIJ*)aij->A->data;
    m    = aij->A->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a;
    row  = mat->rmap->rstart;
    for (i=0; i<ai[m]; i++) aj[i] += mat->cmap->rstart;
    for (i=0; i<m; i++) {
      ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],aj,a,INSERT_VALUES);CHKERRQ(ierr);
      row++;
      a += ai[i+1]-ai[i]; aj += ai[i+1]-ai[i];
    }
    aj = Aloc->j;
    for (i=0; i<ai[m]; i++) aj[i] -= mat->cmap->rstart;

    /* copy over the B part */
    Aloc = (Mat_SeqAIJ*)aij->B->data;
    m    = aij->B->rmap->n;  ai = Aloc->i; aj = Aloc->j; a = Aloc->a;
    row  = mat->rmap->rstart;
    ierr = PetscMalloc1(ai[m]+1,&cols);CHKERRQ(ierr);
    ct   = cols;
    for (i=0; i<ai[m]; i++) cols[i] = aij->garray[aj[i]];
    for (i=0; i<m; i++) {
      ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],cols,a,INSERT_VALUES);CHKERRQ(ierr);
      row++;
      a += ai[i+1]-ai[i]; cols += ai[i+1]-ai[i];
    }
    ierr = PetscFree(ct);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    /*
       Everyone has to call to draw the matrix since the graphics waits are
       synchronized across all processors that share the PetscDraw object
    */
    ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr);
    if (!rank) {
      ierr = PetscObjectSetName((PetscObject)((Mat_MPIAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr);
      ierr = MatView_SeqAIJ(((Mat_MPIAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr);
    }
    ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr);
    ierr = PetscViewerFlush(viewer);CHKERRQ(ierr);
    ierr = MatDestroy(&A);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatView_MPIAIJ(Mat mat,PetscViewer viewer)
{
  PetscErrorCode ierr;
  PetscBool      iascii,isdraw,issocket,isbinary;

  PetscFunctionBegin;
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr);
  if (iascii || isdraw || isbinary || issocket) {
    ierr = MatView_MPIAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatSOR_MPIAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx)
{
  Mat_MPIAIJ     *mat = (Mat_MPIAIJ*)matin->data;
  PetscErrorCode ierr;
  Vec            bb1 = 0;
  PetscBool      hasop;

  PetscFunctionBegin;
  if (flag == SOR_APPLY_UPPER) {
    ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr);
    PetscFunctionReturn(0);
  }

  if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) {
    ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr);
  }

  if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) {
    if (flag & SOR_ZERO_INITIAL_GUESS) {
      ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr);
      its--;
    }

    while (its--) {
      ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
      ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);

      /* update rhs: bb1 = bb - B*x */
      ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr);
      ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr);

      /* local sweep */
      ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr);
    }
  } else if (flag & SOR_LOCAL_FORWARD_SWEEP) {
    if (flag & SOR_ZERO_INITIAL_GUESS) {
      ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr);
      its--;
    }
    while (its--) {
      ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
      ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);

      /* update rhs: bb1 = bb - B*x */
      ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr);
      ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr);

      /* local sweep */
      ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr);
    }
  } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) {
    if (flag & SOR_ZERO_INITIAL_GUESS) {
      ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr);
      its--;
    }
    while (its--) {
      ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
      ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);

      /* update rhs: bb1 = bb - B*x */
      ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr);
      ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr);

      /* local sweep */
      ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr);
    }
  } else if (flag & SOR_EISENSTAT) {
    Vec xx1;

    ierr = VecDuplicate(bb,&xx1);CHKERRQ(ierr);
    ierr = (*mat->A->ops->sor)(mat->A,bb,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP),fshift,lits,1,xx);CHKERRQ(ierr);

    ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    if (!mat->diag) {
      ierr = MatCreateVecs(matin,&mat->diag,NULL);CHKERRQ(ierr);
      ierr = MatGetDiagonal(matin,mat->diag);CHKERRQ(ierr);
    }
    ierr = MatHasOperation(matin,MATOP_MULT_DIAGONAL_BLOCK,&hasop);CHKERRQ(ierr);
    if (hasop) {
      ierr = MatMultDiagonalBlock(matin,xx,bb1);CHKERRQ(ierr);
    } else {
      ierr = VecPointwiseMult(bb1,mat->diag,xx);CHKERRQ(ierr);
    }
    ierr = VecAYPX(bb1,(omega-2.0)/omega,bb);CHKERRQ(ierr);

    ierr = MatMultAdd(mat->B,mat->lvec,bb1,bb1);CHKERRQ(ierr);

    /* local sweep */
    ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP),fshift,lits,1,xx1);CHKERRQ(ierr);
    ierr = VecAXPY(xx,1.0,xx1);CHKERRQ(ierr);
    ierr = VecDestroy(&xx1);CHKERRQ(ierr);
  } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel SOR not supported");

  ierr = VecDestroy(&bb1);CHKERRQ(ierr);

  matin->factorerrortype = mat->A->factorerrortype;
  PetscFunctionReturn(0);
}

PetscErrorCode MatPermute_MPIAIJ(Mat A,IS rowp,IS colp,Mat *B)
{
  Mat            aA,aB,Aperm;
  const PetscInt *rwant,*cwant,*gcols,*ai,*bi,*aj,*bj;
  PetscScalar    *aa,*ba;
  PetscInt       i,j,m,n,ng,anz,bnz,*dnnz,*onnz,*tdnnz,*tonnz,*rdest,*cdest,*work,*gcdest;
  PetscSF        rowsf,sf;
  IS             parcolp = NULL;
  PetscBool      done;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
  ierr = ISGetIndices(rowp,&rwant);CHKERRQ(ierr);
  ierr = ISGetIndices(colp,&cwant);CHKERRQ(ierr);
  ierr = PetscMalloc3(PetscMax(m,n),&work,m,&rdest,n,&cdest);CHKERRQ(ierr);

  /* Invert row permutation to find out where my rows should go */
  ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&rowsf);CHKERRQ(ierr);
  ierr = PetscSFSetGraphLayout(rowsf,A->rmap,A->rmap->n,NULL,PETSC_OWN_POINTER,rwant);CHKERRQ(ierr);
  ierr = PetscSFSetFromOptions(rowsf);CHKERRQ(ierr);
  for (i=0; i<m; i++) work[i] = A->rmap->rstart + i;
  ierr = PetscSFReduceBegin(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr);
  ierr = PetscSFReduceEnd(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr);

  /* Invert column permutation to find out where my columns should go */
  ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr);
  ierr = PetscSFSetGraphLayout(sf,A->cmap,A->cmap->n,NULL,PETSC_OWN_POINTER,cwant);CHKERRQ(ierr);
  ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr);
  for (i=0; i<n; i++) work[i] = A->cmap->rstart + i;
  ierr = PetscSFReduceBegin(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr);
  ierr = PetscSFReduceEnd(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&sf);CHKERRQ(ierr);

  ierr = ISRestoreIndices(rowp,&rwant);CHKERRQ(ierr);
  ierr = ISRestoreIndices(colp,&cwant);CHKERRQ(ierr);
  ierr = MatMPIAIJGetSeqAIJ(A,&aA,&aB,&gcols);CHKERRQ(ierr);

  /* Find out where my gcols should go */
  ierr = MatGetSize(aB,NULL,&ng);CHKERRQ(ierr);
  ierr = PetscMalloc1(ng,&gcdest);CHKERRQ(ierr);
  ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr);
  ierr = PetscSFSetGraphLayout(sf,A->cmap,ng,NULL,PETSC_OWN_POINTER,gcols);CHKERRQ(ierr);
  ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&sf);CHKERRQ(ierr);

  ierr = PetscCalloc4(m,&dnnz,m,&onnz,m,&tdnnz,m,&tonnz);CHKERRQ(ierr);
  ierr = MatGetRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr);
  ierr = MatGetRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr);
  for (i=0; i<m; i++) {
    PetscInt row = rdest[i],rowner;
    ierr = PetscLayoutFindOwner(A->rmap,row,&rowner);CHKERRQ(ierr);
    for (j=ai[i]; j<ai[i+1]; j++) {
      PetscInt cowner,col = cdest[aj[j]];
      ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); /* Could build an index for the columns to eliminate this search */
      if (rowner == cowner) dnnz[i]++;
      else onnz[i]++;
    }
    for (j=bi[i]; j<bi[i+1]; j++) {
      PetscInt cowner,col = gcdest[bj[j]];
      ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr);
      if (rowner == cowner) dnnz[i]++;
      else onnz[i]++;
    }
  }
  ierr = PetscSFBcastBegin(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&rowsf);CHKERRQ(ierr);

  ierr = MatCreateAIJ(PetscObjectComm((PetscObject)A),A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N,0,tdnnz,0,tonnz,&Aperm);CHKERRQ(ierr);
  ierr = MatSeqAIJGetArray(aA,&aa);CHKERRQ(ierr);
  ierr = MatSeqAIJGetArray(aB,&ba);CHKERRQ(ierr);
  for (i=0; i<m; i++) {
    PetscInt *acols = dnnz,*bcols = onnz; /* Repurpose now-unneeded arrays */
    PetscInt j0,rowlen;
    rowlen = ai[i+1] - ai[i];
    for (j0=j=0; j<rowlen; j0=j) { /* rowlen could be larger than number of rows m, so sum in batches */
      for ( ; j<PetscMin(rowlen,j0+m); j++) acols[j-j0] = cdest[aj[ai[i]+j]];
      ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,acols,aa+ai[i]+j0,INSERT_VALUES);CHKERRQ(ierr);
    }
    rowlen = bi[i+1] - bi[i];
    for (j0=j=0; j<rowlen; j0=j) {
      for ( ; j<PetscMin(rowlen,j0+m); j++) bcols[j-j0] = gcdest[bj[bi[i]+j]];
      ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,bcols,ba+bi[i]+j0,INSERT_VALUES);CHKERRQ(ierr);
    }
  }
  ierr = MatAssemblyBegin(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatRestoreRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr);
  ierr = MatRestoreRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr);
  ierr = MatSeqAIJRestoreArray(aA,&aa);CHKERRQ(ierr);
  ierr = MatSeqAIJRestoreArray(aB,&ba);CHKERRQ(ierr);
  ierr = PetscFree4(dnnz,onnz,tdnnz,tonnz);CHKERRQ(ierr);
  ierr = PetscFree3(work,rdest,cdest);CHKERRQ(ierr);
  ierr = PetscFree(gcdest);CHKERRQ(ierr);
  if (parcolp) {ierr = ISDestroy(&colp);CHKERRQ(ierr);}
  *B = Aperm;
  PetscFunctionReturn(0);
}

PetscErrorCode  MatGetGhosts_MPIAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[])
{
  Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MatGetSize(aij->B,NULL,nghosts);CHKERRQ(ierr);
  if (ghosts) *ghosts = aij->garray;
  PetscFunctionReturn(0);
}

PetscErrorCode MatGetInfo_MPIAIJ(Mat matin,MatInfoType flag,MatInfo *info)
{
  Mat_MPIAIJ     *mat = (Mat_MPIAIJ*)matin->data;
  Mat            A    = mat->A,B = mat->B;
  PetscErrorCode ierr;
  PetscReal      isend[5],irecv[5];

  PetscFunctionBegin;
  info->block_size = 1.0;
  ierr             = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr);

  isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded;
  isend[3] = info->memory;  isend[4] = info->mallocs;

  ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr);

  isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded;
  isend[3] += info->memory;  isend[4] += info->mallocs;
  if (flag == MAT_LOCAL) {
    info->nz_used      = isend[0];
    info->nz_allocated = isend[1];
    info->nz_unneeded  = isend[2];
    info->memory       = isend[3];
    info->mallocs      = isend[4];
  } else if (flag == MAT_GLOBAL_MAX) {
    ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr);

    info->nz_used      = irecv[0];
    info->nz_allocated = irecv[1];
    info->nz_unneeded  = irecv[2];
    info->memory       = irecv[3];
    info->mallocs      = irecv[4];
  } else if (flag == MAT_GLOBAL_SUM) {
    ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr);

    info->nz_used      = irecv[0];
    info->nz_allocated = irecv[1];
    info->nz_unneeded  = irecv[2];
    info->memory       = irecv[3];
    info->mallocs      = irecv[4];
  }
  info->fill_ratio_given  = 0; /* no parallel LU/ILU/Cholesky */
  info->fill_ratio_needed = 0;
  info->factor_mallocs    = 0;
  PetscFunctionReturn(0);
}

PetscErrorCode MatSetOption_MPIAIJ(Mat A,MatOption op,PetscBool flg)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  switch (op) {
  case MAT_NEW_NONZERO_LOCATIONS:
  case MAT_NEW_NONZERO_ALLOCATION_ERR:
  case MAT_UNUSED_NONZERO_LOCATION_ERR:
  case MAT_KEEP_NONZERO_PATTERN:
  case MAT_NEW_NONZERO_LOCATION_ERR:
  case MAT_USE_INODES:
  case MAT_IGNORE_ZERO_ENTRIES:
    MatCheckPreallocated(A,1);
    ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr);
    ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr);
    break;
  case MAT_ROW_ORIENTED:
    MatCheckPreallocated(A,1);
    a->roworiented = flg;

    ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr);
    ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr);
    break;
  case MAT_NEW_DIAGONALS:
    ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr);
    break;
  case MAT_IGNORE_OFF_PROC_ENTRIES:
    a->donotstash = flg;
    break;
  case MAT_SPD:
    A->spd_set = PETSC_TRUE;
    A->spd     = flg;
    if (flg) {
      A->symmetric                  = PETSC_TRUE;
      A->structurally_symmetric     = PETSC_TRUE;
      A->symmetric_set              = PETSC_TRUE;
      A->structurally_symmetric_set = PETSC_TRUE;
    }
    break;
  case MAT_SYMMETRIC:
    MatCheckPreallocated(A,1);
    ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr);
    break;
  case MAT_STRUCTURALLY_SYMMETRIC:
    MatCheckPreallocated(A,1);
    ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr);
    break;
  case MAT_HERMITIAN:
    MatCheckPreallocated(A,1);
    ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr);
    break;
  case MAT_SYMMETRY_ETERNAL:
    MatCheckPreallocated(A,1);
    ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr);
    break;
  case MAT_SUBMAT_SINGLEIS:
    A->submat_singleis = flg;
    break;
  case MAT_STRUCTURE_ONLY:
    /* The option is handled directly by MatSetOption() */
    break;
  default:
    SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatGetRow_MPIAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
{
  Mat_MPIAIJ     *mat = (Mat_MPIAIJ*)matin->data;
  PetscScalar    *vworkA,*vworkB,**pvA,**pvB,*v_p;
  PetscErrorCode ierr;
  PetscInt       i,*cworkA,*cworkB,**pcA,**pcB,cstart = matin->cmap->rstart;
  PetscInt       nztot,nzA,nzB,lrow,rstart = matin->rmap->rstart,rend = matin->rmap->rend;
  PetscInt       *cmap,*idx_p;

  PetscFunctionBegin;
  if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active");
  mat->getrowactive = PETSC_TRUE;

  if (!mat->rowvalues && (idx || v)) {
    /*
        allocate enough space to hold information from the longest row.
    */
    Mat_SeqAIJ *Aa = (Mat_SeqAIJ*)mat->A->data,*Ba = (Mat_SeqAIJ*)mat->B->data;
    PetscInt   max = 1,tmp;
    for (i=0; i<matin->rmap->n; i++) {
      tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i];
      if (max < tmp) max = tmp;
    }
    ierr = PetscMalloc2(max,&mat->rowvalues,max,&mat->rowindices);CHKERRQ(ierr);
  }

  if (row < rstart || row >= rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only local rows");
  lrow = row - rstart;

  pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB;
  if (!v)   {pvA = 0; pvB = 0;}
  if (!idx) {pcA = 0; if (!v) pcB = 0;}
  ierr  = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr);
  ierr  = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr);
  nztot = nzA + nzB;

  cmap = mat->garray;
  if (v  || idx) {
    if (nztot) {
      /* Sort by increasing column numbers, assuming A and B already sorted */
      PetscInt imark = -1;
      if (v) {
        *v = v_p = mat->rowvalues;
        for (i=0; i<nzB; i++) {
          if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i];
          else break;
        }
        imark = i;
        for (i=0; i<nzA; i++)     v_p[imark+i] = vworkA[i];
        for (i=imark; i<nzB; i++) v_p[nzA+i]   = vworkB[i];
      }
      if (idx) {
        *idx = idx_p = mat->rowindices;
        if (imark > -1) {
          for (i=0; i<imark; i++) {
            idx_p[i] = cmap[cworkB[i]];
          }
        } else {
          for (i=0; i<nzB; i++) {
            if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]];
            else break;
          }
          imark = i;
        }
        for (i=0; i<nzA; i++)     idx_p[imark+i] = cstart + cworkA[i];
        for (i=imark; i<nzB; i++) idx_p[nzA+i]   = cmap[cworkB[i]];
      }
    } else {
      if (idx) *idx = 0;
      if (v)   *v   = 0;
    }
  }
  *nz  = nztot;
  ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr);
  ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
{
  Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data;

  PetscFunctionBegin;
  if (!aij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow() must be called first");
  aij->getrowactive = PETSC_FALSE;
  PetscFunctionReturn(0);
}

PetscErrorCode MatNorm_MPIAIJ(Mat mat,NormType type,PetscReal *norm)
{
  Mat_MPIAIJ     *aij  = (Mat_MPIAIJ*)mat->data;
  Mat_SeqAIJ     *amat = (Mat_SeqAIJ*)aij->A->data,*bmat = (Mat_SeqAIJ*)aij->B->data;
  PetscErrorCode ierr;
  PetscInt       i,j,cstart = mat->cmap->rstart;
  PetscReal      sum = 0.0;
  MatScalar      *v;

  PetscFunctionBegin;
  if (aij->size == 1) {
    ierr =  MatNorm(aij->A,type,norm);CHKERRQ(ierr);
  } else {
    if (type == NORM_FROBENIUS) {
      v = amat->a;
      for (i=0; i<amat->nz; i++) {
        sum += PetscRealPart(PetscConj(*v)*(*v)); v++;
      }
      v = bmat->a;
      for (i=0; i<bmat->nz; i++) {
        sum += PetscRealPart(PetscConj(*v)*(*v)); v++;
      }
      ierr  = MPIU_Allreduce(&sum,norm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
      *norm = PetscSqrtReal(*norm);
      ierr = PetscLogFlops(2*amat->nz+2*bmat->nz);CHKERRQ(ierr);
    } else if (type == NORM_1) { /* max column norm */
      PetscReal *tmp,*tmp2;
      PetscInt  *jj,*garray = aij->garray;
      ierr  = PetscCalloc1(mat->cmap->N+1,&tmp);CHKERRQ(ierr);
      ierr  = PetscMalloc1(mat->cmap->N+1,&tmp2);CHKERRQ(ierr);
      *norm = 0.0;
      v     = amat->a; jj = amat->j;
      for (j=0; j<amat->nz; j++) {
        tmp[cstart + *jj++] += PetscAbsScalar(*v);  v++;
      }
      v = bmat->a; jj = bmat->j;
      for (j=0; j<bmat->nz; j++) {
        tmp[garray[*jj++]] += PetscAbsScalar(*v); v++;
      }
      ierr = MPIU_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
      for (j=0; j<mat->cmap->N; j++) {
        if (tmp2[j] > *norm) *norm = tmp2[j];
      }
      ierr = PetscFree(tmp);CHKERRQ(ierr);
      ierr = PetscFree(tmp2);CHKERRQ(ierr);
      ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr);
    } else if (type == NORM_INFINITY) { /* max row norm */
      PetscReal ntemp = 0.0;
      for (j=0; j<aij->A->rmap->n; j++) {
        v   = amat->a + amat->i[j];
        sum = 0.0;
        for (i=0; i<amat->i[j+1]-amat->i[j]; i++) {
          sum += PetscAbsScalar(*v); v++;
        }
        v = bmat->a + bmat->i[j];
        for (i=0; i<bmat->i[j+1]-bmat->i[j]; i++) {
          sum += PetscAbsScalar(*v); v++;
        }
        if (sum > ntemp) ntemp = sum;
      }
      ierr = MPIU_Allreduce(&ntemp,norm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
      ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr);
    } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for two norm");
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatTranspose_MPIAIJ(Mat A,MatReuse reuse,Mat *matout)
{
  Mat_MPIAIJ     *a   = (Mat_MPIAIJ*)A->data;
  Mat_SeqAIJ     *Aloc=(Mat_SeqAIJ*)a->A->data,*Bloc=(Mat_SeqAIJ*)a->B->data;
  PetscErrorCode ierr;
  PetscInt       M      = A->rmap->N,N = A->cmap->N,ma,na,mb,nb,*ai,*aj,*bi,*bj,row,*cols,*cols_tmp,i;
  PetscInt       cstart = A->cmap->rstart,ncol;
  Mat            B;
  MatScalar      *array;

  PetscFunctionBegin;
  if (reuse == MAT_INPLACE_MATRIX && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place");

  ma = A->rmap->n; na = A->cmap->n; mb = a->B->rmap->n; nb = a->B->cmap->n;
  ai = Aloc->i; aj = Aloc->j;
  bi = Bloc->i; bj = Bloc->j;
  if (reuse == MAT_INITIAL_MATRIX || *matout == A) {
    PetscInt             *d_nnz,*g_nnz,*o_nnz;
    PetscSFNode          *oloc;
    PETSC_UNUSED PetscSF sf;

    ierr = PetscMalloc4(na,&d_nnz,na,&o_nnz,nb,&g_nnz,nb,&oloc);CHKERRQ(ierr);
    /* compute d_nnz for preallocation */
    ierr = PetscMemzero(d_nnz,na*sizeof(PetscInt));CHKERRQ(ierr);
    for (i=0; i<ai[ma]; i++) {
      d_nnz[aj[i]]++;
      aj[i] += cstart; /* global col index to be used by MatSetValues() */
    }
    /* compute local off-diagonal contributions */
    ierr = PetscMemzero(g_nnz,nb*sizeof(PetscInt));CHKERRQ(ierr);
    for (i=0; i<bi[ma]; i++) g_nnz[bj[i]]++;
    /* map those to global */
    ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr);
    ierr = PetscSFSetGraphLayout(sf,A->cmap,nb,NULL,PETSC_USE_POINTER,a->garray);CHKERRQ(ierr);
    ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr);
    ierr = PetscMemzero(o_nnz,na*sizeof(PetscInt));CHKERRQ(ierr);
    ierr = PetscSFReduceBegin(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr);
    ierr = PetscSFReduceEnd(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr);
    ierr = PetscSFDestroy(&sf);CHKERRQ(ierr);

    ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr);
    ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr);
    ierr = MatSetBlockSizes(B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr);
    ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr);
    ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr);
    ierr = PetscFree4(d_nnz,o_nnz,g_nnz,oloc);CHKERRQ(ierr);
  } else {
    B    = *matout;
    ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
    for (i=0; i<ai[ma]; i++) aj[i] += cstart; /* global col index to be used by MatSetValues() */
  }

  /* copy over the A part */
  array = Aloc->a;
  row   = A->rmap->rstart;
  for (i=0; i<ma; i++) {
    ncol = ai[i+1]-ai[i];
    ierr = MatSetValues(B,ncol,aj,1,&row,array,INSERT_VALUES);CHKERRQ(ierr);
    row++;
    array += ncol; aj += ncol;
  }
  aj = Aloc->j;
  for (i=0; i<ai[ma]; i++) aj[i] -= cstart; /* resume local col index */

  /* copy over the B part */
  ierr  = PetscCalloc1(bi[mb],&cols);CHKERRQ(ierr);
  array = Bloc->a;
  row   = A->rmap->rstart;
  for (i=0; i<bi[mb]; i++) cols[i] = a->garray[bj[i]];
  cols_tmp = cols;
  for (i=0; i<mb; i++) {
    ncol = bi[i+1]-bi[i];
    ierr = MatSetValues(B,ncol,cols_tmp,1,&row,array,INSERT_VALUES);CHKERRQ(ierr);
    row++;
    array += ncol; cols_tmp += ncol;
  }
  ierr = PetscFree(cols);CHKERRQ(ierr);

  ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) {
    *matout = B;
  } else {
    ierr = MatHeaderMerge(A,&B);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat,Vec ll,Vec rr)
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  Mat            a    = aij->A,b = aij->B;
  PetscErrorCode ierr;
  PetscInt       s1,s2,s3;

  PetscFunctionBegin;
  ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr);
  if (rr) {
    ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr);
    if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size");
    /* Overlap communication with computation. */
    ierr = VecScatterBegin(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  }
  if (ll) {
    ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr);
    if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size");
    ierr = (*b->ops->diagonalscale)(b,ll,0);CHKERRQ(ierr);
  }
  /* scale  the diagonal block */
  ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr);

  if (rr) {
    /* Do a scatter end and then right scale the off-diagonal block */
    ierr = VecScatterEnd(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = (*b->ops->diagonalscale)(b,0,aij->lvec);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MatSetUnfactored(a->A);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatEqual_MPIAIJ(Mat A,Mat B,PetscBool  *flag)
{
  Mat_MPIAIJ     *matB = (Mat_MPIAIJ*)B->data,*matA = (Mat_MPIAIJ*)A->data;
  Mat            a,b,c,d;
  PetscBool      flg;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  a = matA->A; b = matA->B;
  c = matB->A; d = matB->B;

  ierr = MatEqual(a,c,&flg);CHKERRQ(ierr);
  if (flg) {
    ierr = MatEqual(b,d,&flg);CHKERRQ(ierr);
  }
  ierr = MPIU_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatCopy_MPIAIJ(Mat A,Mat B,MatStructure str)
{
  PetscErrorCode ierr;
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  Mat_MPIAIJ     *b = (Mat_MPIAIJ*)B->data;

  PetscFunctionBegin;
  /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */
  if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) {
    /* because of the column compression in the off-processor part of the matrix a->B,
       the number of columns in a->B and b->B may be different, hence we cannot call
       the MatCopy() directly on the two parts. If need be, we can provide a more
       efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices
       then copying the submatrices */
    ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr);
  } else {
    ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr);
    ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatSetUp_MPIAIJ(Mat A)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr =  MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
   Computes the number of nonzeros per row needed for preallocation when X and Y
   have different nonzero structure.
*/
PetscErrorCode MatAXPYGetPreallocation_MPIX_private(PetscInt m,const PetscInt *xi,const PetscInt *xj,const PetscInt *xltog,const PetscInt *yi,const PetscInt *yj,const PetscInt *yltog,PetscInt *nnz)
{
  PetscInt       i,j,k,nzx,nzy;

  PetscFunctionBegin;
  /* Set the number of nonzeros in the new matrix */
  for (i=0; i<m; i++) {
    const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i];
    nzx = xi[i+1] - xi[i];
    nzy = yi[i+1] - yi[i];
    nnz[i] = 0;
    for (j=0,k=0; j<nzx; j++) {                   /* Point in X */
      for (; k<nzy && yltog[yjj[k]]<xltog[xjj[j]]; k++) nnz[i]++; /* Catch up to X */
      if (k<nzy && yltog[yjj[k]]==xltog[xjj[j]]) k++;             /* Skip duplicate */
      nnz[i]++;
    }
    for (; k<nzy; k++) nnz[i]++;
  }
  PetscFunctionReturn(0);
}

/* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */
static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz)
{
  PetscErrorCode ierr;
  PetscInt       m = Y->rmap->N;
  Mat_SeqAIJ     *x = (Mat_SeqAIJ*)X->data;
  Mat_SeqAIJ     *y = (Mat_SeqAIJ*)Y->data;

  PetscFunctionBegin;
  ierr = MatAXPYGetPreallocation_MPIX_private(m,x->i,x->j,xltog,y->i,y->j,yltog,nnz);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatAXPY_MPIAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str)
{
  PetscErrorCode ierr;
  Mat_MPIAIJ     *xx = (Mat_MPIAIJ*)X->data,*yy = (Mat_MPIAIJ*)Y->data;
  PetscBLASInt   bnz,one=1;
  Mat_SeqAIJ     *x,*y;

  PetscFunctionBegin;
  if (str == SAME_NONZERO_PATTERN) {
    PetscScalar alpha = a;
    x    = (Mat_SeqAIJ*)xx->A->data;
    ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr);
    y    = (Mat_SeqAIJ*)yy->A->data;
    PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one));
    x    = (Mat_SeqAIJ*)xx->B->data;
    y    = (Mat_SeqAIJ*)yy->B->data;
    ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr);
    PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one));
    ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr);
  } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */
    ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr);
  } else {
    Mat      B;
    PetscInt *nnz_d,*nnz_o;
    ierr = PetscMalloc1(yy->A->rmap->N,&nnz_d);CHKERRQ(ierr);
    ierr = PetscMalloc1(yy->B->rmap->N,&nnz_o);CHKERRQ(ierr);
    ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr);
    ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr);
    ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr);
    ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr);
    ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr);
    ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr);
    ierr = MatAXPYGetPreallocation_MPIAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr);
    ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr);
    ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr);
    ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr);
    ierr = PetscFree(nnz_d);CHKERRQ(ierr);
    ierr = PetscFree(nnz_o);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

extern PetscErrorCode  MatConjugate_SeqAIJ(Mat);

PetscErrorCode  MatConjugate_MPIAIJ(Mat mat)
{
#if defined(PETSC_USE_COMPLEX)
  PetscErrorCode ierr;
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;

  PetscFunctionBegin;
  ierr = MatConjugate_SeqAIJ(aij->A);CHKERRQ(ierr);
  ierr = MatConjugate_SeqAIJ(aij->B);CHKERRQ(ierr);
#else
  PetscFunctionBegin;
#endif
  PetscFunctionReturn(0);
}

PetscErrorCode MatRealPart_MPIAIJ(Mat A)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MatRealPart(a->A);CHKERRQ(ierr);
  ierr = MatRealPart(a->B);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MatImaginaryPart(a->A);CHKERRQ(ierr);
  ierr = MatImaginaryPart(a->B);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[])
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;
  PetscInt       i,*idxb = 0;
  PetscScalar    *va,*vb;
  Vec            vtmp;

  PetscFunctionBegin;
  ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr);
  ierr = VecGetArray(v,&va);CHKERRQ(ierr);
  if (idx) {
    for (i=0; i<A->rmap->n; i++) {
      if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart;
    }
  }

  ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr);
  if (idx) {
    ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr);
  }
  ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr);
  ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr);

  for (i=0; i<A->rmap->n; i++) {
    if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) {
      va[i] = vb[i];
      if (idx) idx[i] = a->garray[idxb[i]];
    }
  }

  ierr = VecRestoreArray(v,&va);CHKERRQ(ierr);
  ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr);
  ierr = PetscFree(idxb);CHKERRQ(ierr);
  ierr = VecDestroy(&vtmp);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[])
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;
  PetscInt       i,*idxb = 0;
  PetscScalar    *va,*vb;
  Vec            vtmp;

  PetscFunctionBegin;
  ierr = MatGetRowMinAbs(a->A,v,idx);CHKERRQ(ierr);
  ierr = VecGetArray(v,&va);CHKERRQ(ierr);
  if (idx) {
    for (i=0; i<A->cmap->n; i++) {
      if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart;
    }
  }

  ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr);
  if (idx) {
    ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr);
  }
  ierr = MatGetRowMinAbs(a->B,vtmp,idxb);CHKERRQ(ierr);
  ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr);

  for (i=0; i<A->rmap->n; i++) {
    if (PetscAbsScalar(va[i]) > PetscAbsScalar(vb[i])) {
      va[i] = vb[i];
      if (idx) idx[i] = a->garray[idxb[i]];
    }
  }

  ierr = VecRestoreArray(v,&va);CHKERRQ(ierr);
  ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr);
  ierr = PetscFree(idxb);CHKERRQ(ierr);
  ierr = VecDestroy(&vtmp);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[])
{
  Mat_MPIAIJ     *mat   = (Mat_MPIAIJ*) A->data;
  PetscInt       n      = A->rmap->n;
  PetscInt       cstart = A->cmap->rstart;
  PetscInt       *cmap  = mat->garray;
  PetscInt       *diagIdx, *offdiagIdx;
  Vec            diagV, offdiagV;
  PetscScalar    *a, *diagA, *offdiagA;
  PetscInt       r;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr);
  ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &diagV);CHKERRQ(ierr);
  ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &offdiagV);CHKERRQ(ierr);
  ierr = MatGetRowMin(mat->A, diagV,    diagIdx);CHKERRQ(ierr);
  ierr = MatGetRowMin(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr);
  ierr = VecGetArray(v,        &a);CHKERRQ(ierr);
  ierr = VecGetArray(diagV,    &diagA);CHKERRQ(ierr);
  ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr);
  for (r = 0; r < n; ++r) {
    if (PetscAbsScalar(diagA[r]) <= PetscAbsScalar(offdiagA[r])) {
      a[r]   = diagA[r];
      idx[r] = cstart + diagIdx[r];
    } else {
      a[r]   = offdiagA[r];
      idx[r] = cmap[offdiagIdx[r]];
    }
  }
  ierr = VecRestoreArray(v,        &a);CHKERRQ(ierr);
  ierr = VecRestoreArray(diagV,    &diagA);CHKERRQ(ierr);
  ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr);
  ierr = VecDestroy(&diagV);CHKERRQ(ierr);
  ierr = VecDestroy(&offdiagV);CHKERRQ(ierr);
  ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[])
{
  Mat_MPIAIJ     *mat   = (Mat_MPIAIJ*) A->data;
  PetscInt       n      = A->rmap->n;
  PetscInt       cstart = A->cmap->rstart;
  PetscInt       *cmap  = mat->garray;
  PetscInt       *diagIdx, *offdiagIdx;
  Vec            diagV, offdiagV;
  PetscScalar    *a, *diagA, *offdiagA;
  PetscInt       r;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr);
  ierr = VecCreateSeq(PETSC_COMM_SELF, n, &diagV);CHKERRQ(ierr);
  ierr = VecCreateSeq(PETSC_COMM_SELF, n, &offdiagV);CHKERRQ(ierr);
  ierr = MatGetRowMax(mat->A, diagV,    diagIdx);CHKERRQ(ierr);
  ierr = MatGetRowMax(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr);
  ierr = VecGetArray(v,        &a);CHKERRQ(ierr);
  ierr = VecGetArray(diagV,    &diagA);CHKERRQ(ierr);
  ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr);
  for (r = 0; r < n; ++r) {
    if (PetscAbsScalar(diagA[r]) >= PetscAbsScalar(offdiagA[r])) {
      a[r]   = diagA[r];
      idx[r] = cstart + diagIdx[r];
    } else {
      a[r]   = offdiagA[r];
      idx[r] = cmap[offdiagIdx[r]];
    }
  }
  ierr = VecRestoreArray(v,        &a);CHKERRQ(ierr);
  ierr = VecRestoreArray(diagV,    &diagA);CHKERRQ(ierr);
  ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr);
  ierr = VecDestroy(&diagV);CHKERRQ(ierr);
  ierr = VecDestroy(&offdiagV);CHKERRQ(ierr);
  ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat,Mat *newmat)
{
  PetscErrorCode ierr;
  Mat            *dummy;

  PetscFunctionBegin;
  ierr    = MatCreateSubMatrix_MPIAIJ_All(mat,MAT_DO_NOT_GET_VALUES,MAT_INITIAL_MATRIX,&dummy);CHKERRQ(ierr);
  *newmat = *dummy;
  ierr    = PetscFree(dummy);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode  MatInvertBlockDiagonal_MPIAIJ(Mat A,const PetscScalar **values)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*) A->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr);
  A->factorerrortype = a->A->factorerrortype;
  PetscFunctionReturn(0);
}

static PetscErrorCode  MatSetRandom_MPIAIJ(Mat x,PetscRandom rctx)
{
  PetscErrorCode ierr;
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)x->data;

  PetscFunctionBegin;
  ierr = MatSetRandom(aij->A,rctx);CHKERRQ(ierr);
  ierr = MatSetRandom(aij->B,rctx);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ(Mat A,PetscBool sc)
{
  PetscFunctionBegin;
  if (sc) A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ_Scalable;
  else A->ops->increaseoverlap    = MatIncreaseOverlap_MPIAIJ;
  PetscFunctionReturn(0);
}

/*@
   MatMPIAIJSetUseScalableIncreaseOverlap - Determine if the matrix uses a scalable algorithm to compute the overlap

   Collective on Mat

   Input Parameters:
+    A - the matrix
-    sc - PETSC_TRUE indicates use the scalable algorithm (default is not to use the scalable algorithm)

 Level: advanced

@*/
PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap(Mat A,PetscBool sc)
{
  PetscErrorCode       ierr;

  PetscFunctionBegin;
  ierr = PetscTryMethod(A,"MatMPIAIJSetUseScalableIncreaseOverlap_C",(Mat,PetscBool),(A,sc));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatSetFromOptions_MPIAIJ(PetscOptionItems *PetscOptionsObject,Mat A)
{
  PetscErrorCode       ierr;
  PetscBool            sc = PETSC_FALSE,flg;

  PetscFunctionBegin;
  ierr = PetscOptionsHead(PetscOptionsObject,"MPIAIJ options");CHKERRQ(ierr);
  ierr = PetscObjectOptionsBegin((PetscObject)A);
    if (A->ops->increaseoverlap == MatIncreaseOverlap_MPIAIJ_Scalable) sc = PETSC_TRUE;
    ierr = PetscOptionsBool("-mat_increase_overlap_scalable","Use a scalable algorithm to compute the overlap","MatIncreaseOverlap",sc,&sc,&flg);CHKERRQ(ierr);
    if (flg) {
      ierr = MatMPIAIJSetUseScalableIncreaseOverlap(A,sc);CHKERRQ(ierr);
    }
  ierr = PetscOptionsEnd();CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatShift_MPIAIJ(Mat Y,PetscScalar a)
{
  PetscErrorCode ierr;
  Mat_MPIAIJ     *maij = (Mat_MPIAIJ*)Y->data;
  Mat_SeqAIJ     *aij = (Mat_SeqAIJ*)maij->A->data;

  PetscFunctionBegin;
  if (!Y->preallocated) {
    ierr = MatMPIAIJSetPreallocation(Y,1,NULL,0,NULL);CHKERRQ(ierr);
  } else if (!aij->nz) {
    PetscInt nonew = aij->nonew;
    ierr = MatSeqAIJSetPreallocation(maij->A,1,NULL);CHKERRQ(ierr);
    aij->nonew = nonew;
  }
  ierr = MatShift_Basic(Y,a);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatMissingDiagonal_MPIAIJ(Mat A,PetscBool  *missing,PetscInt *d)
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices");
  ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr);
  if (d) {
    PetscInt rstart;
    ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr);
    *d += rstart;

  }
  PetscFunctionReturn(0);
}


/* -------------------------------------------------------------------*/
static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ,
                                       MatGetRow_MPIAIJ,
                                       MatRestoreRow_MPIAIJ,
                                       MatMult_MPIAIJ,
                                /* 4*/ MatMultAdd_MPIAIJ,
                                       MatMultTranspose_MPIAIJ,
                                       MatMultTransposeAdd_MPIAIJ,
                                       0,
                                       0,
                                       0,
                                /*10*/ 0,
                                       0,
                                       0,
                                       MatSOR_MPIAIJ,
                                       MatTranspose_MPIAIJ,
                                /*15*/ MatGetInfo_MPIAIJ,
                                       MatEqual_MPIAIJ,
                                       MatGetDiagonal_MPIAIJ,
                                       MatDiagonalScale_MPIAIJ,
                                       MatNorm_MPIAIJ,
                                /*20*/ MatAssemblyBegin_MPIAIJ,
                                       MatAssemblyEnd_MPIAIJ,
                                       MatSetOption_MPIAIJ,
                                       MatZeroEntries_MPIAIJ,
                                /*24*/ MatZeroRows_MPIAIJ,
                                       0,
                                       0,
                                       0,
                                       0,
                                /*29*/ MatSetUp_MPIAIJ,
                                       0,
                                       0,
                                       MatGetDiagonalBlock_MPIAIJ,
                                       0,
                                /*34*/ MatDuplicate_MPIAIJ,
                                       0,
                                       0,
                                       0,
                                       0,
                                /*39*/ MatAXPY_MPIAIJ,
                                       MatCreateSubMatrices_MPIAIJ,
                                       MatIncreaseOverlap_MPIAIJ,
                                       MatGetValues_MPIAIJ,
                                       MatCopy_MPIAIJ,
                                /*44*/ MatGetRowMax_MPIAIJ,
                                       MatScale_MPIAIJ,
                                       MatShift_MPIAIJ,
                                       MatDiagonalSet_MPIAIJ,
                                       MatZeroRowsColumns_MPIAIJ,
                                /*49*/ MatSetRandom_MPIAIJ,
                                       0,
                                       0,
                                       0,
                                       0,
                                /*54*/ MatFDColoringCreate_MPIXAIJ,
                                       0,
                                       MatSetUnfactored_MPIAIJ,
                                       MatPermute_MPIAIJ,
                                       0,
                                /*59*/ MatCreateSubMatrix_MPIAIJ,
                                       MatDestroy_MPIAIJ,
                                       MatView_MPIAIJ,
                                       0,
                                       MatMatMatMult_MPIAIJ_MPIAIJ_MPIAIJ,
                                /*64*/ MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ,
                                       MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ,
                                       0,
                                       0,
                                       0,
                                /*69*/ MatGetRowMaxAbs_MPIAIJ,
                                       MatGetRowMinAbs_MPIAIJ,
                                       0,
                                       0,
                                       0,
                                       0,
                                /*75*/ MatFDColoringApply_AIJ,
                                       MatSetFromOptions_MPIAIJ,
                                       0,
                                       0,
                                       MatFindZeroDiagonals_MPIAIJ,
                                /*80*/ 0,
                                       0,
                                       0,
                                /*83*/ MatLoad_MPIAIJ,
                                       0,
                                       0,
                                       0,
                                       0,
                                       0,
                                /*89*/ MatMatMult_MPIAIJ_MPIAIJ,
                                       MatMatMultSymbolic_MPIAIJ_MPIAIJ,
                                       MatMatMultNumeric_MPIAIJ_MPIAIJ,
                                       MatPtAP_MPIAIJ_MPIAIJ,
                                       MatPtAPSymbolic_MPIAIJ_MPIAIJ,
                                /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ,
                                       0,
                                       0,
                                       0,
                                       0,
                                /*99*/ 0,
                                       0,
                                       0,
                                       MatConjugate_MPIAIJ,
                                       0,
                                /*104*/MatSetValuesRow_MPIAIJ,
                                       MatRealPart_MPIAIJ,
                                       MatImaginaryPart_MPIAIJ,
                                       0,
                                       0,
                                /*109*/0,
                                       0,
                                       MatGetRowMin_MPIAIJ,
                                       0,
                                       MatMissingDiagonal_MPIAIJ,
                                /*114*/MatGetSeqNonzeroStructure_MPIAIJ,
                                       0,
                                       MatGetGhosts_MPIAIJ,
                                       0,
                                       0,
                                /*119*/0,
                                       0,
                                       0,
                                       0,
                                       MatGetMultiProcBlock_MPIAIJ,
                                /*124*/MatFindNonzeroRows_MPIAIJ,
                                       MatGetColumnNorms_MPIAIJ,
                                       MatInvertBlockDiagonal_MPIAIJ,
                                       0,
                                       MatCreateSubMatricesMPI_MPIAIJ,
                                /*129*/0,
                                       MatTransposeMatMult_MPIAIJ_MPIAIJ,
                                       MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ,
                                       MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ,
                                       0,
                                /*134*/0,
                                       0,
                                       MatRARt_MPIAIJ_MPIAIJ,
                                       0,
                                       0,
                                /*139*/MatSetBlockSizes_MPIAIJ,
                                       0,
                                       0,
                                       MatFDColoringSetUp_MPIXAIJ,
                                       MatFindOffBlockDiagonalEntries_MPIAIJ,
                                /*144*/MatCreateMPIMatConcatenateSeqMat_MPIAIJ
};

/* ----------------------------------------------------------------------------------------*/

PetscErrorCode  MatStoreValues_MPIAIJ(Mat mat)
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MatStoreValues(aij->A);CHKERRQ(ierr);
  ierr = MatStoreValues(aij->B);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode  MatRetrieveValues_MPIAIJ(Mat mat)
{
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr);
  ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode  MatMPIAIJSetPreallocation_MPIAIJ(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[])
{
  Mat_MPIAIJ     *b;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr);
  ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr);
  b = (Mat_MPIAIJ*)B->data;

#if defined(PETSC_USE_CTABLE)
  ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr);
#else
  ierr = PetscFree(b->colmap);CHKERRQ(ierr);
#endif
  ierr = PetscFree(b->garray);CHKERRQ(ierr);
  ierr = VecDestroy(&b->lvec);CHKERRQ(ierr);
  ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr);

  /* Because the B will have been resized we simply destroy it and create a new one each time */
  ierr = MatDestroy(&b->B);CHKERRQ(ierr);
  ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr);
  ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr);
  ierr = MatSetBlockSizesFromMats(b->B,B,B);CHKERRQ(ierr);
  ierr = MatSetType(b->B,MATSEQAIJ);CHKERRQ(ierr);
  ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr);

  if (!B->preallocated) {
    ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr);
    ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr);
    ierr = MatSetBlockSizesFromMats(b->A,B,B);CHKERRQ(ierr);
    ierr = MatSetType(b->A,MATSEQAIJ);CHKERRQ(ierr);
    ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr);
  }

  ierr = MatSeqAIJSetPreallocation(b->A,d_nz,d_nnz);CHKERRQ(ierr);
  ierr = MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz);CHKERRQ(ierr);
  B->preallocated  = PETSC_TRUE;
  B->was_assembled = PETSC_FALSE;
  B->assembled     = PETSC_FALSE;;
  PetscFunctionReturn(0);
}

PetscErrorCode MatDuplicate_MPIAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat)
{
  Mat            mat;
  Mat_MPIAIJ     *a,*oldmat = (Mat_MPIAIJ*)matin->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  *newmat = 0;
  ierr    = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr);
  ierr    = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr);
  ierr    = MatSetBlockSizesFromMats(mat,matin,matin);CHKERRQ(ierr);
  ierr    = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr);
  ierr    = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr);
  a       = (Mat_MPIAIJ*)mat->data;

  mat->factortype   = matin->factortype;
  mat->assembled    = PETSC_TRUE;
  mat->insertmode   = NOT_SET_VALUES;
  mat->preallocated = PETSC_TRUE;

  a->size         = oldmat->size;
  a->rank         = oldmat->rank;
  a->donotstash   = oldmat->donotstash;
  a->roworiented  = oldmat->roworiented;
  a->rowindices   = 0;
  a->rowvalues    = 0;
  a->getrowactive = PETSC_FALSE;

  ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr);
  ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr);

  if (oldmat->colmap) {
#if defined(PETSC_USE_CTABLE)
    ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr);
#else
    ierr = PetscMalloc1(mat->cmap->N,&a->colmap);CHKERRQ(ierr);
    ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr);
    ierr = PetscMemcpy(a->colmap,oldmat->colmap,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr);
#endif
  } else a->colmap = 0;
  if (oldmat->garray) {
    PetscInt len;
    len  = oldmat->B->cmap->n;
    ierr = PetscMalloc1(len+1,&a->garray);CHKERRQ(ierr);
    ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr);
    if (len) { ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); }
  } else a->garray = 0;

  ierr    = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr);
  ierr    = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr);
  ierr    = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr);
  ierr    = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr);
  ierr    = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr);
  ierr    = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr);
  ierr    = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr);
  ierr    = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr);
  ierr    = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr);
  *newmat = mat;
  PetscFunctionReturn(0);
}

PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer)
{
  PetscScalar    *vals,*svals;
  MPI_Comm       comm;
  PetscErrorCode ierr;
  PetscMPIInt    rank,size,tag = ((PetscObject)viewer)->tag;
  PetscInt       i,nz,j,rstart,rend,mmax,maxnz = 0;
  PetscInt       header[4],*rowlengths = 0,M,N,m,*cols;
  PetscInt       *ourlens = NULL,*procsnz = NULL,*offlens = NULL,jj,*mycols,*smycols;
  PetscInt       cend,cstart,n,*rowners;
  int            fd;
  PetscInt       bs = newMat->rmap->bs;

  PetscFunctionBegin;
  /* force binary viewer to load .info file if it has not yet done so */
  ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
  ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr);
  if (!rank) {
    ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr);
    if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object");
    if (header[3] < 0) SETERRQ(PetscObjectComm((PetscObject)newMat),PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as MATMPIAIJ");
  }

  ierr = PetscOptionsBegin(comm,NULL,"Options for loading MATMPIAIJ matrix","Mat");CHKERRQ(ierr);
  ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsEnd();CHKERRQ(ierr);
  if (bs < 0) bs = 1;

  ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr);
  M    = header[1]; N = header[2];

  /* If global sizes are set, check if they are consistent with that given in the file */
  if (newMat->rmap->N >= 0 && newMat->rmap->N != M) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of rows:Matrix in file has (%D) and input matrix has (%D)",newMat->rmap->N,M);
  if (newMat->cmap->N >=0 && newMat->cmap->N != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of cols:Matrix in file has (%D) and input matrix has (%D)",newMat->cmap->N,N);

  /* determine ownership of all (block) rows */
  if (M%bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows (%d) and block size (%d)",M,bs);
  if (newMat->rmap->n < 0) m = bs*((M/bs)/size + (((M/bs) % size) > rank));    /* PETSC_DECIDE */
  else m = newMat->rmap->n; /* Set by user */

  ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr);
  ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr);

  /* First process needs enough room for process with most rows */
  if (!rank) {
    mmax = rowners[1];
    for (i=2; i<=size; i++) {
      mmax = PetscMax(mmax, rowners[i]);
    }
  } else mmax = -1;             /* unused, but compilers complain */

  rowners[0] = 0;
  for (i=2; i<=size; i++) {
    rowners[i] += rowners[i-1];
  }
  rstart = rowners[rank];
  rend   = rowners[rank+1];

  /* distribute row lengths to all processors */
  ierr = PetscMalloc2(m,&ourlens,m,&offlens);CHKERRQ(ierr);
  if (!rank) {
    ierr = PetscBinaryRead(fd,ourlens,m,PETSC_INT);CHKERRQ(ierr);
    ierr = PetscMalloc1(mmax,&rowlengths);CHKERRQ(ierr);
    ierr = PetscCalloc1(size,&procsnz);CHKERRQ(ierr);
    for (j=0; j<m; j++) {
      procsnz[0] += ourlens[j];
    }
    for (i=1; i<size; i++) {
      ierr = PetscBinaryRead(fd,rowlengths,rowners[i+1]-rowners[i],PETSC_INT);CHKERRQ(ierr);
      /* calculate the number of nonzeros on each processor */
      for (j=0; j<rowners[i+1]-rowners[i]; j++) {
        procsnz[i] += rowlengths[j];
      }
      ierr = MPIULong_Send(rowlengths,rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr);
    }
    ierr = PetscFree(rowlengths);CHKERRQ(ierr);
  } else {
    ierr = MPIULong_Recv(ourlens,m,MPIU_INT,0,tag,comm);CHKERRQ(ierr);
  }

  if (!rank) {
    /* determine max buffer needed and allocate it */
    maxnz = 0;
    for (i=0; i<size; i++) {
      maxnz = PetscMax(maxnz,procsnz[i]);
    }
    ierr = PetscMalloc1(maxnz,&cols);CHKERRQ(ierr);

    /* read in my part of the matrix column indices  */
    nz   = procsnz[0];
    ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr);
    ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr);

    /* read in every one elses and ship off */
    for (i=1; i<size; i++) {
      nz   = procsnz[i];
      ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr);
      ierr = MPIULong_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr);
    }
    ierr = PetscFree(cols);CHKERRQ(ierr);
  } else {
    /* determine buffer space needed for message */
    nz = 0;
    for (i=0; i<m; i++) {
      nz += ourlens[i];
    }
    ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr);

    /* receive message of column indices*/
    ierr = MPIULong_Recv(mycols,nz,MPIU_INT,0,tag,comm);CHKERRQ(ierr);
  }

  /* determine column ownership if matrix is not square */
  if (N != M) {
    if (newMat->cmap->n < 0) n = N/size + ((N % size) > rank);
    else n = newMat->cmap->n;
    ierr   = MPI_Scan(&n,&cend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr);
    cstart = cend - n;
  } else {
    cstart = rstart;
    cend   = rend;
    n      = cend - cstart;
  }

  /* loop over local rows, determining number of off diagonal entries */
  ierr = PetscMemzero(offlens,m*sizeof(PetscInt));CHKERRQ(ierr);
  jj   = 0;
  for (i=0; i<m; i++) {
    for (j=0; j<ourlens[i]; j++) {
      if (mycols[jj] < cstart || mycols[jj] >= cend) offlens[i]++;
      jj++;
    }
  }

  for (i=0; i<m; i++) {
    ourlens[i] -= offlens[i];
  }
  ierr = MatSetSizes(newMat,m,n,M,N);CHKERRQ(ierr);

  if (bs > 1) {ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr);}

  ierr = MatMPIAIJSetPreallocation(newMat,0,ourlens,0,offlens);CHKERRQ(ierr);

  for (i=0; i<m; i++) {
    ourlens[i] += offlens[i];
  }

  if (!rank) {
    ierr = PetscMalloc1(maxnz+1,&vals);CHKERRQ(ierr);

    /* read in my part of the matrix numerical values  */
    nz   = procsnz[0];
    ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr);

    /* insert into matrix */
    jj      = rstart;
    smycols = mycols;
    svals   = vals;
    for (i=0; i<m; i++) {
      ierr     = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr);
      smycols += ourlens[i];
      svals   += ourlens[i];
      jj++;
    }

    /* read in other processors and ship out */
    for (i=1; i<size; i++) {
      nz   = procsnz[i];
      ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr);
      ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr);
    }
    ierr = PetscFree(procsnz);CHKERRQ(ierr);
  } else {
    /* receive numeric values */
    ierr = PetscMalloc1(nz+1,&vals);CHKERRQ(ierr);

    /* receive message of values*/
    ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr);

    /* insert into matrix */
    jj      = rstart;
    smycols = mycols;
    svals   = vals;
    for (i=0; i<m; i++) {
      ierr     = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr);
      smycols += ourlens[i];
      svals   += ourlens[i];
      jj++;
    }
  }
  ierr = PetscFree2(ourlens,offlens);CHKERRQ(ierr);
  ierr = PetscFree(vals);CHKERRQ(ierr);
  ierr = PetscFree(mycols);CHKERRQ(ierr);
  ierr = PetscFree(rowners);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/* Not scalable because of ISAllGather() unless getting all columns. */
PetscErrorCode ISGetSeqIS_Private(Mat mat,IS iscol,IS *isseq)
{
  PetscErrorCode ierr;
  IS             iscol_local;
  PetscBool      isstride;
  PetscMPIInt    lisstride=0,gisstride;

  PetscFunctionBegin;
  /* check if we are grabbing all columns*/
  ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&isstride);CHKERRQ(ierr);

  if (isstride) {
    PetscInt  start,len,mstart,mlen;
    ierr = ISStrideGetInfo(iscol,&start,NULL);CHKERRQ(ierr);
    ierr = ISGetLocalSize(iscol,&len);CHKERRQ(ierr);
    ierr = MatGetOwnershipRangeColumn(mat,&mstart,&mlen);CHKERRQ(ierr);
    if (mstart == start && mlen-mstart == len) lisstride = 1;
  }

  ierr = MPIU_Allreduce(&lisstride,&gisstride,1,MPI_INT,MPI_MIN,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
  if (gisstride) {
    PetscInt N;
    ierr = MatGetSize(mat,NULL,&N);CHKERRQ(ierr);
    ierr = ISCreateStride(PetscObjectComm((PetscObject)mat),N,0,1,&iscol_local);CHKERRQ(ierr);
    ierr = ISSetIdentity(iscol_local);CHKERRQ(ierr);
    ierr = PetscInfo(mat,"Optimizing for obtaining all columns of the matrix; skipping ISAllGather()\n");CHKERRQ(ierr);
  } else {
    PetscInt cbs;
    ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr);
    ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr);
    ierr = ISSetBlockSize(iscol_local,cbs);CHKERRQ(ierr);
  }

  *isseq = iscol_local;
  PetscFunctionReturn(0);
}

/*
 Used by MatCreateSubMatrix_MPIAIJ_SameRowColDist() to avoid ISAllGather() and global size of iscol_local
 (see MatCreateSubMatrix_MPIAIJ_nonscalable)

 Input Parameters:
   mat - matrix
   isrow - parallel row index set; its local indices are a subset of local columns of mat,
           i.e., mat->rstart <= isrow[i] < mat->rend
   iscol - parallel column index set; its local indices are a subset of local columns of mat,
           i.e., mat->cstart <= iscol[i] < mat->cend
 Output Parameter:
   isrow_d,iscol_d - sequential row and column index sets for retrieving mat->A
   iscol_o - sequential column index set for retrieving mat->B
   garray - column map; garray[i] indicates global location of iscol_o[i] in iscol
 */
PetscErrorCode ISGetSeqIS_SameColDist_Private(Mat mat,IS isrow,IS iscol,IS *isrow_d,IS *iscol_d,IS *iscol_o,const PetscInt *garray[])
{
  PetscErrorCode ierr;
  Vec            x,cmap;
  const PetscInt *is_idx;
  PetscScalar    *xarray,*cmaparray;
  PetscInt       ncols,isstart,*idx,m,rstart,*cmap1,count;
  Mat_MPIAIJ     *a=(Mat_MPIAIJ*)mat->data;
  Mat            B=a->B;
  Vec            lvec=a->lvec,lcmap;
  PetscInt       i,cstart,cend,Bn=B->cmap->N;
  MPI_Comm       comm;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr);
  ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr);

  /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */
  ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr);
  ierr = VecDuplicate(x,&cmap);CHKERRQ(ierr);
  ierr = VecSet(x,-1.0);CHKERRQ(ierr);

  /* Get start indices */
  ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr);
  isstart -= ncols;
  ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr);

  ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr);
  ierr = VecGetArray(x,&xarray);CHKERRQ(ierr);
  ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr);
  ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr);
  for (i=0; i<ncols; i++) {
    xarray[is_idx[i]-cstart]    = (PetscScalar)is_idx[i];
    cmaparray[is_idx[i]-cstart] = i + isstart;      /* global index of iscol[i] */
    idx[i]                      = is_idx[i]-cstart; /* local index of iscol[i]  */
  }
  ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr);
  ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr);
  ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr);

  /* Get iscol_d */
  ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,iscol_d);CHKERRQ(ierr);
  ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr);
  ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr);

  /* Get isrow_d */
  ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr);
  rstart = mat->rmap->rstart;
  ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr);
  ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr);
  for (i=0; i<m; i++) idx[i] = is_idx[i]-rstart;
  ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr);

  ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_OWN_POINTER,isrow_d);CHKERRQ(ierr);
  ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr);
  ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr);

  /* (2) Scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */
  ierr = VecScatterBegin(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);

  ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr);

  ierr = VecScatterEnd(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterBegin(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterEnd(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);

  /* (3) create sequential iscol_o (a subset of iscol) and isgarray */
  /* off-process column indices */
  count = 0;
  ierr = PetscMalloc1(Bn,&idx);CHKERRQ(ierr);
  ierr = PetscMalloc1(Bn,&cmap1);CHKERRQ(ierr);

  ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr);
  ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr);
  for (i=0; i<Bn; i++) {
    if (PetscRealPart(xarray[i]) > -1.0) {
      idx[count]     = i;                   /* local column index in off-diagonal part B */
      cmap1[count++] = (PetscInt)PetscRealPart(cmaparray[i]);  /* column index in submat */
    }
  }
  ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr);
  ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr);

  ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,iscol_o);CHKERRQ(ierr);
  /* cannot ensure iscol_o has same blocksize as iscol! */

  ierr = PetscFree(idx);CHKERRQ(ierr);

  *garray = cmap1;

  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = VecDestroy(&cmap);CHKERRQ(ierr);
  ierr = VecDestroy(&lcmap);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/* isrow and iscol have same processor distribution as mat, output *submat is a submatrix of local mat */
PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowColDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *submat)
{
  PetscErrorCode ierr;
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)mat->data,*asub;
  Mat            M = NULL;
  MPI_Comm       comm;
  IS             iscol_d,isrow_d,iscol_o;
  Mat            Asub = NULL,Bsub = NULL;
  PetscInt       n;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr);

  if (call == MAT_REUSE_MATRIX) {
    /* Retrieve isrow_d, iscol_d and iscol_o from submat */
    ierr = PetscObjectQuery((PetscObject)*submat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr);
    if (!isrow_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"isrow_d passed in was not used before, cannot reuse");

    ierr = PetscObjectQuery((PetscObject)*submat,"iscol_d",(PetscObject*)&iscol_d);CHKERRQ(ierr);
    if (!iscol_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_d passed in was not used before, cannot reuse");

    ierr = PetscObjectQuery((PetscObject)*submat,"iscol_o",(PetscObject*)&iscol_o);CHKERRQ(ierr);
    if (!iscol_o) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_o passed in was not used before, cannot reuse");

    /* Update diagonal and off-diagonal portions of submat */
    asub = (Mat_MPIAIJ*)(*submat)->data;
    ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->A);CHKERRQ(ierr);
    ierr = ISGetLocalSize(iscol_o,&n);CHKERRQ(ierr);
    if (n) {
      ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->B);CHKERRQ(ierr);
    }
    ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  } else { /* call == MAT_INITIAL_MATRIX) */
    const PetscInt *garray;
    PetscInt        BsubN;

    /* Create isrow_d, iscol_d, iscol_o and isgarray (replace isgarray with array?) */
    ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&isrow_d,&iscol_d,&iscol_o,&garray);CHKERRQ(ierr);

    /* Create local submatrices Asub and Bsub */
    ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Asub);CHKERRQ(ierr);
    ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Bsub);CHKERRQ(ierr);

    /* Create submatrix M */
    ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray,&M);CHKERRQ(ierr);

    /* If Bsub has empty columns, compress iscol_o such that it will retrieve condensed Bsub from a->B during reuse */
    asub = (Mat_MPIAIJ*)M->data;

    ierr = ISGetLocalSize(iscol_o,&BsubN);CHKERRQ(ierr);
    n = asub->B->cmap->N;
    if (BsubN > n) {
      /* This case can be tested using ~petsc/src/tao/bound/examples/tutorials/runplate2_3 */
      const PetscInt *idx;
      PetscInt       i,j,*idx_new,*subgarray = asub->garray;
      ierr = PetscInfo2(M,"submatrix Bn %D != BsubN %D, update iscol_o\n",n,BsubN);CHKERRQ(ierr);

      ierr = PetscMalloc1(n,&idx_new);CHKERRQ(ierr);
      j = 0;
      ierr = ISGetIndices(iscol_o,&idx);CHKERRQ(ierr);
      for (i=0; i<n; i++) {
        if (j >= BsubN) break;
        while (subgarray[i] > garray[j]) j++;

        if (subgarray[i] == garray[j]) {
          idx_new[i] = idx[j++];
        } else SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"subgarray[%D]=%D cannot < garray[%D]=%D",i,subgarray[i],j,garray[j]);
      }
      ierr = ISRestoreIndices(iscol_o,&idx);CHKERRQ(ierr);

      ierr = ISDestroy(&iscol_o);CHKERRQ(ierr);
      ierr = ISCreateGeneral(PETSC_COMM_SELF,n,idx_new,PETSC_OWN_POINTER,&iscol_o);CHKERRQ(ierr);

    } else if (BsubN < n) {
      SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Columns of Bsub cannot be smaller than B's",BsubN,asub->B->cmap->N);
    }

    ierr = PetscFree(garray);CHKERRQ(ierr);
    *submat = M;

    /* Save isrow_d, iscol_d and iscol_o used in processor for next request */
    ierr = PetscObjectCompose((PetscObject)M,"isrow_d",(PetscObject)isrow_d);CHKERRQ(ierr);
    ierr = ISDestroy(&isrow_d);CHKERRQ(ierr);

    ierr = PetscObjectCompose((PetscObject)M,"iscol_d",(PetscObject)iscol_d);CHKERRQ(ierr);
    ierr = ISDestroy(&iscol_d);CHKERRQ(ierr);

    ierr = PetscObjectCompose((PetscObject)M,"iscol_o",(PetscObject)iscol_o);CHKERRQ(ierr);
    ierr = ISDestroy(&iscol_o);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat)
{
  PetscErrorCode ierr;
  IS             iscol_local,isrow_d;
  PetscInt       csize;
  PetscInt       n,i,j,start,end;
  PetscBool      sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2];
  MPI_Comm       comm;

  PetscFunctionBegin;
  /* If isrow has same processor distribution as mat,
     call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */
  if (call == MAT_REUSE_MATRIX) {
    ierr = PetscObjectQuery((PetscObject)*newmat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr);
    if (isrow_d) {
      sameRowDist  = PETSC_TRUE;
      tsameDist[1] = PETSC_TRUE; /* sameColDist */
    } else {
      ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr);
      if (iscol_local) {
        sameRowDist  = PETSC_TRUE;
        tsameDist[1] = PETSC_FALSE; /* !sameColDist */
      }
    }
  } else {
    /* Check if isrow has same processor distribution as mat */
    sameDist[0] = PETSC_FALSE;
    ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr);
    if (!n) {
      sameDist[0] = PETSC_TRUE;
    } else {
      ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr);
      ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr);
      if (i >= start && j < end) {
        sameDist[0] = PETSC_TRUE;
      }
    }

    /* Check if iscol has same processor distribution as mat */
    sameDist[1] = PETSC_FALSE;
    ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr);
    if (!n) {
      sameDist[1] = PETSC_TRUE;
    } else {
      ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr);
      ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr);
      if (i >= start && j < end) sameDist[1] = PETSC_TRUE;
    }

    ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr);
    ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr);
    sameRowDist = tsameDist[0];
  }

  if (sameRowDist) {
    if (tsameDist[1]) { /* sameRowDist & sameColDist */
      /* isrow and iscol have same processor distribution as mat */
      ierr = MatCreateSubMatrix_MPIAIJ_SameRowColDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr);
    } else { /* sameRowDist */
      /* isrow has same processor distribution as mat */
      ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr);
    }
    PetscFunctionReturn(0);
  }

  /* General case: iscol -> iscol_local which has global size of iscol */
  if (call == MAT_REUSE_MATRIX) {
    ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr);
    if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse");
  } else {
    ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr);
  }

  ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr);
  ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr);

  if (call == MAT_INITIAL_MATRIX) {
    ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr);
    ierr = ISDestroy(&iscol_local);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

/*@C
     MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal"
         and "off-diagonal" part of the matrix in CSR format.

   Collective on MPI_Comm

   Input Parameters:
+  comm - MPI communicator
.  A - "diagonal" portion of matrix
.  B - "off-diagonal" portion of matrix, may have empty columns, will be destroyed by this routine
-  garray - global index of B columns

   Output Parameter:
.   mat - the matrix, with input A as its local diagonal matrix
   Level: advanced

   Notes:
       See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix.
       A becomes part of output mat, B is destroyed by this routine. The user cannot use A and B anymore.

.seealso: MatCreateMPIAIJWithSplitArrays()
@*/
PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat)
{
  PetscErrorCode ierr;
  Mat_MPIAIJ     *maij;
  Mat_SeqAIJ     *b=(Mat_SeqAIJ*)B->data,*bnew;
  PetscInt       *oi=b->i,*oj=b->j,i,nz,col;
  PetscScalar    *oa=b->a;
  Mat            Bnew;
  PetscInt       m,n,N;

  PetscFunctionBegin;
  ierr = MatCreate(comm,mat);CHKERRQ(ierr);
  ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr);
  if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %D != Bm %D",m,B->rmap->N);
  if (A->rmap->bs != B->rmap->bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"A row bs %D != B row bs %D",A->rmap->bs,B->rmap->bs);
  /* remove check below; When B is created using iscol_o from ISGetSeqIS_SameColDist_Private(), its bs may not be same as A */
  /* if (A->cmap->bs != B->cmap->bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"A column bs %D != B column bs %D",A->cmap->bs,B->cmap->bs); */

  /* Get global columns of mat */
  ierr = MPIU_Allreduce(&n,&N,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr);

  ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr);
  ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr);
  ierr = MatSetBlockSizes(*mat,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr);
  maij = (Mat_MPIAIJ*)(*mat)->data;

  (*mat)->preallocated = PETSC_TRUE;

  ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr);
  ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr);

  /* Set A as diagonal portion of *mat */
  maij->A = A;

  nz = oi[m];
  for (i=0; i<nz; i++) {
    col   = oj[i];
    oj[i] = garray[col];
  }

   /* Set Bnew as off-diagonal portion of *mat */
  ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Bnew);CHKERRQ(ierr);
  bnew        = (Mat_SeqAIJ*)Bnew->data;
  bnew->maxnz = b->maxnz; /* allocated nonzeros of B */
  maij->B     = Bnew;

  if (B->rmap->N != Bnew->rmap->N) SETERRQ2(PETSC_COMM_SELF,0,"BN %d != BnewN %d",B->rmap->N,Bnew->rmap->N);

  b->singlemalloc = PETSC_FALSE; /* B arrays are shared by Bnew */
  b->free_a       = PETSC_FALSE;
  b->free_ij      = PETSC_FALSE;
  ierr = MatDestroy(&B);CHKERRQ(ierr);

  bnew->singlemalloc = PETSC_TRUE; /* arrays will be freed by MatDestroy(&Bnew) */
  bnew->free_a       = PETSC_TRUE;
  bnew->free_ij      = PETSC_TRUE;

  /* condense columns of maij->B */
  ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr);
  ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*);

PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat)
{
  PetscErrorCode ierr;
  PetscInt       i,m,n,rstart,row,rend,nz,j,bs,cbs;
  PetscInt       *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal;
  Mat_MPIAIJ     *a=(Mat_MPIAIJ*)mat->data;
  Mat            M,Msub,B=a->B;
  MatScalar      *aa;
  Mat_SeqAIJ     *aij;
  PetscInt       *garray = a->garray,*colsub,Ncols;
  PetscInt       count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend;
  IS             iscol_sub,iscmap;
  const PetscInt *is_idx,*cmap;
  PetscBool      allcolumns=PETSC_FALSE;
  IS             iscol_local=NULL;
  MPI_Comm       comm;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr);

  if (call == MAT_REUSE_MATRIX) {
    ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr);
    if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse");
    ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr);

    ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr);
    if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse");

    ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr);
    if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse");

    ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr);

  } else { /* call == MAT_INITIAL_MATRIX) */
    PetscBool flg;

    ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr);
    ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr);

    /* (1) iscol -> nonscalable iscol_local */
    ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr);
    ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */
    if (n != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != Ncols %d",n,Ncols);

    /* Check for special case: each processor gets entire matrix columns */
    ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr);
    if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE;
    if (allcolumns) {
      iscol_sub = iscol_local;
      ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr);
      ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr);

    } else {
      /* (2) iscol_local -> iscol_sub and iscmap */
      PetscInt *idx,*cmap1,k;

      /* implementation below requires iscol_local be sorted, it can have duplicate indices */
      ierr = ISSorted(iscol_local,&flg);CHKERRQ(ierr);
      if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsorted iscol_local is not implemented yet");

      ierr = PetscMalloc1(Ncols,&idx);CHKERRQ(ierr);
      ierr = PetscMalloc1(Ncols,&cmap1);CHKERRQ(ierr);
      ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr);
      count = 0;
      k     = 0;
      for (i=0; i<Ncols; i++) {
        j = is_idx[i];
        if (j >= cstart && j < cend) {
          /* diagonal part of mat */
          idx[count]     = j;
          cmap1[count++] = i; /* column index in submat */
        } else if (Bn) {
          /* off-diagonal part of mat */
          if (j == garray[k]) {
            idx[count]     = j;
            cmap1[count++] = i;  /* column index in submat */
          } else if (j > garray[k]) {
            while (j > garray[k] && k < Bn-1) k++;
            if (j == garray[k]) {
              idx[count]     = j;
              cmap1[count++] = i; /* column index in submat */
            }
          }
        }
      }
      ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr);

      ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_OWN_POINTER,&iscol_sub);CHKERRQ(ierr);
      ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr);
      ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr);

      ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_OWN_POINTER,&iscmap);CHKERRQ(ierr);
    }

    /* (3) Create sequential Msub */
    ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr);
  }

  ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr);
  aij  = (Mat_SeqAIJ*)(Msub)->data;
  ii   = aij->i;
  ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr);

  /*
      m - number of local rows
      Ncols - number of columns (same on all processors)
      rstart - first row in new global matrix generated
  */
  ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr);

  if (call == MAT_INITIAL_MATRIX) {
    /* (4) Create parallel newmat */
    PetscMPIInt    rank,size;
    PetscInt       csize;

    ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
    ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);

    /*
        Determine the number of non-zeros in the diagonal and off-diagonal
        portions of the matrix in order to do correct preallocation
    */

    /* first get start and end of "diagonal" columns */
    ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr);
    if (csize == PETSC_DECIDE) {
      ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr);
      if (mglobal == Ncols) { /* square matrix */
        nlocal = m;
      } else {
        nlocal = Ncols/size + ((Ncols % size) > rank);
      }
    } else {
      nlocal = csize;
    }
    ierr   = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr);
    rstart = rend - nlocal;
    if (rank == size - 1 && rend != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local column sizes %D do not add up to total number of columns %D",rend,Ncols);

    /* next, compute all the lengths */
    jj    = aij->j;
    ierr  = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr);
    olens = dlens + m;
    for (i=0; i<m; i++) {
      jend = ii[i+1] - ii[i];
      olen = 0;
      dlen = 0;
      for (j=0; j<jend; j++) {
        if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++;
        else dlen++;
        jj++;
      }
      olens[i] = olen;
      dlens[i] = dlen;
    }

    ierr = ISGetBlockSize(isrow,&bs);CHKERRQ(ierr);
    ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr);

    ierr = MatCreate(comm,&M);CHKERRQ(ierr);
    ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,Ncols);CHKERRQ(ierr);
    ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr);
    ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr);
    ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr);
    ierr = PetscFree(dlens);CHKERRQ(ierr);

  } else { /* call == MAT_REUSE_MATRIX */
    M    = *newmat;
    ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr);
    if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request");
    ierr = MatZeroEntries(M);CHKERRQ(ierr);
    /*
         The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly,
       rather than the slower MatSetValues().
    */
    M->was_assembled = PETSC_TRUE;
    M->assembled     = PETSC_FALSE;
  }

  /* (5) Set values of Msub to *newmat */
  ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr);
  ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr);

  jj   = aij->j;
  aa   = aij->a;
  for (i=0; i<m; i++) {
    row = rstart + i;
    nz  = ii[i+1] - ii[i];
    for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]];
    ierr  = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr);
    jj += nz; aa += nz;
  }
  ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr);

  ierr    = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr    = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  ierr = PetscFree(colsub);CHKERRQ(ierr);

  /* save Msub, iscol_sub and iscmap used in processor for next request */
  if (call ==  MAT_INITIAL_MATRIX) {
    *newmat = M;
    ierr = PetscObjectCompose((PetscObject)(*newmat),"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr);
    ierr = MatDestroy(&Msub);CHKERRQ(ierr);

    ierr = PetscObjectCompose((PetscObject)(*newmat),"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr);
    ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr);

    ierr = PetscObjectCompose((PetscObject)(*newmat),"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr);
    ierr = ISDestroy(&iscmap);CHKERRQ(ierr);

    if (iscol_local) {
      ierr = PetscObjectCompose((PetscObject)(*newmat),"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr);
      ierr = ISDestroy(&iscol_local);CHKERRQ(ierr);
    }
  }
  PetscFunctionReturn(0);
}

/*
    Not great since it makes two copies of the submatrix, first an SeqAIJ
  in local and then by concatenating the local matrices the end result.
  Writing it directly would be much like MatCreateSubMatrices_MPIAIJ()

  Note: This requires a sequential iscol with all indices.
*/
PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat)
{
  PetscErrorCode ierr;
  PetscMPIInt    rank,size;
  PetscInt       i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs;
  PetscInt       *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal;
  Mat            M,Mreuse;
  MatScalar      *aa,*vwork;
  MPI_Comm       comm;
  Mat_SeqAIJ     *aij;
  PetscBool      colflag,allcolumns=PETSC_FALSE;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);

  /* Check for special case: each processor gets entire matrix columns */
  ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr);
  ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr);
  if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE;

  if (call ==  MAT_REUSE_MATRIX) {
    ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr);
    if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse");
    ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr);
  } else {
    ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr);
  }

  /*
      m - number of local rows
      n - number of columns (same on all processors)
      rstart - first row in new global matrix generated
  */
  ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr);
  ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr);
  if (call == MAT_INITIAL_MATRIX) {
    aij = (Mat_SeqAIJ*)(Mreuse)->data;
    ii  = aij->i;
    jj  = aij->j;

    /*
        Determine the number of non-zeros in the diagonal and off-diagonal
        portions of the matrix in order to do correct preallocation
    */

    /* first get start and end of "diagonal" columns */
    if (csize == PETSC_DECIDE) {
      ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr);
      if (mglobal == n) { /* square matrix */
        nlocal = m;
      } else {
        nlocal = n/size + ((n % size) > rank);
      }
    } else {
      nlocal = csize;
    }
    ierr   = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr);
    rstart = rend - nlocal;
    if (rank == size - 1 && rend != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local column sizes %D do not add up to total number of columns %D",rend,n);

    /* next, compute all the lengths */
    ierr  = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr);
    olens = dlens + m;
    for (i=0; i<m; i++) {
      jend = ii[i+1] - ii[i];
      olen = 0;
      dlen = 0;
      for (j=0; j<jend; j++) {
        if (*jj < rstart || *jj >= rend) olen++;
        else dlen++;
        jj++;
      }
      olens[i] = olen;
      dlens[i] = dlen;
    }
    ierr = MatCreate(comm,&M);CHKERRQ(ierr);
    ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr);
    ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr);
    ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr);
    ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr);
    ierr = PetscFree(dlens);CHKERRQ(ierr);
  } else {
    PetscInt ml,nl;

    M    = *newmat;
    ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr);
    if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request");
    ierr = MatZeroEntries(M);CHKERRQ(ierr);
    /*
         The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly,
       rather than the slower MatSetValues().
    */
    M->was_assembled = PETSC_TRUE;
    M->assembled     = PETSC_FALSE;
  }
  ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr);
  aij  = (Mat_SeqAIJ*)(Mreuse)->data;
  ii   = aij->i;
  jj   = aij->j;
  aa   = aij->a;
  for (i=0; i<m; i++) {
    row   = rstart + i;
    nz    = ii[i+1] - ii[i];
    cwork = jj;     jj += nz;
    vwork = aa;     aa += nz;
    ierr  = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr);
  }

  ierr    = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr    = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  *newmat = M;

  /* save submatrix used in processor for next request */
  if (call ==  MAT_INITIAL_MATRIX) {
    ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr);
    ierr = MatDestroy(&Mreuse);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[])
{
  PetscInt       m,cstart, cend,j,nnz,i,d;
  PetscInt       *d_nnz,*o_nnz,nnz_max = 0,rstart,ii;
  const PetscInt *JJ;
  PetscScalar    *values;
  PetscErrorCode ierr;
  PetscBool      nooffprocentries;

  PetscFunctionBegin;
  if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]);

  ierr   = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr);
  ierr   = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr);
  m      = B->rmap->n;
  cstart = B->cmap->rstart;
  cend   = B->cmap->rend;
  rstart = B->rmap->rstart;

  ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr);

#if defined(PETSC_USE_DEBUGGING)
  for (i=0; i<m; i++) {
    nnz = Ii[i+1]- Ii[i];
    JJ  = J + Ii[i];
    if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz);
    if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j);
    if (nnz && (JJ[nnz-1] >= B->cmap->N) SETERRRQ3(PETSC_ERR_ARG_WRONGSTATE,"Row %D ends with too large a column index %D (max allowed %D)",i,JJ[nnz-1],B->cmap->N);
  }
#endif

  for (i=0; i<m; i++) {
    nnz     = Ii[i+1]- Ii[i];
    JJ      = J + Ii[i];
    nnz_max = PetscMax(nnz_max,nnz);
    d       = 0;
    for (j=0; j<nnz; j++) {
      if (cstart <= JJ[j] && JJ[j] < cend) d++;
    }
    d_nnz[i] = d;
    o_nnz[i] = nnz - d;
  }
  ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr);
  ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr);

  if (v) values = (PetscScalar*)v;
  else {
    ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr);
  }

  for (i=0; i<m; i++) {
    ii   = i + rstart;
    nnz  = Ii[i+1]- Ii[i];
    ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr);
  }
  nooffprocentries    = B->nooffprocentries;
  B->nooffprocentries = PETSC_TRUE;
  ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  B->nooffprocentries = nooffprocentries;

  if (!v) {
    ierr = PetscFree(values);CHKERRQ(ierr);
  }
  ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@
   MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format
   (the default parallel PETSc format).

   Collective on MPI_Comm

   Input Parameters:
+  B - the matrix
.  i - the indices into j for the start of each local row (starts with zero)
.  j - the column indices for each local row (starts with zero)
-  v - optional values in the matrix

   Level: developer

   Notes:
       The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc;
     thus you CANNOT change the matrix entries by changing the values of a[] after you have
     called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays.

       The i and j indices are 0 based, and i indices are indices corresponding to the local j array.

       The format which is used for the sparse matrix input, is equivalent to a
    row-major ordering.. i.e for the following matrix, the input data expected is
    as shown

$        1 0 0
$        2 0 3     P0
$       -------
$        4 5 6     P1
$
$     Process0 [P0]: rows_owned=[0,1]
$        i =  {0,1,3}  [size = nrow+1  = 2+1]
$        j =  {0,0,2}  [size = 3]
$        v =  {1,2,3}  [size = 3]
$
$     Process1 [P1]: rows_owned=[2]
$        i =  {0,3}    [size = nrow+1  = 1+1]
$        j =  {0,1,2}  [size = 3]
$        v =  {4,5,6}  [size = 3]

.keywords: matrix, aij, compressed row, sparse, parallel

.seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ,
          MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays()
@*/
PetscErrorCode  MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[])
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
   MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format
   (the default parallel PETSc format).  For good matrix assembly performance
   the user should preallocate the matrix storage by setting the parameters
   d_nz (or d_nnz) and o_nz (or o_nnz).  By setting these parameters accurately,
   performance can be increased by more than a factor of 50.

   Collective on MPI_Comm

   Input Parameters:
+  B - the matrix
.  d_nz  - number of nonzeros per row in DIAGONAL portion of local submatrix
           (same value is used for all local rows)
.  d_nnz - array containing the number of nonzeros in the various rows of the
           DIAGONAL portion of the local submatrix (possibly different for each row)
           or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure.
           The size of this array is equal to the number of local rows, i.e 'm'.
           For matrices that will be factored, you must leave room for (and set)
           the diagonal entry even if it is zero.
.  o_nz  - number of nonzeros per row in the OFF-DIAGONAL portion of local
           submatrix (same value is used for all local rows).
-  o_nnz - array containing the number of nonzeros in the various rows of the
           OFF-DIAGONAL portion of the local submatrix (possibly different for
           each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero
           structure. The size of this array is equal to the number
           of local rows, i.e 'm'.

   If the *_nnz parameter is given then the *_nz parameter is ignored

   The AIJ format (also called the Yale sparse matrix format or
   compressed row storage (CSR)), is fully compatible with standard Fortran 77
   storage.  The stored row and column indices begin with zero.
   See Users-Manual: ch_mat for details.

   The parallel matrix is partitioned such that the first m0 rows belong to
   process 0, the next m1 rows belong to process 1, the next m2 rows belong
   to process 2 etc.. where m0,m1,m2... are the input parameter 'm'.

   The DIAGONAL portion of the local submatrix of a processor can be defined
   as the submatrix which is obtained by extraction the part corresponding to
   the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the
   first row that belongs to the processor, r2 is the last row belonging to
   the this processor, and c1-c2 is range of indices of the local part of a
   vector suitable for applying the matrix to.  This is an mxn matrix.  In the
   common case of a square matrix, the row and column ranges are the same and
   the DIAGONAL part is also square. The remaining portion of the local
   submatrix (mxN) constitute the OFF-DIAGONAL portion.

   If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored.

   You can call MatGetInfo() to get information on how effective the preallocation was;
   for example the fields mallocs,nz_allocated,nz_used,nz_unneeded;
   You can also run with the option -info and look for messages with the string
   malloc in them to see if additional memory allocation was needed.

   Example usage:

   Consider the following 8x8 matrix with 34 non-zero values, that is
   assembled across 3 processors. Lets assume that proc0 owns 3 rows,
   proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown
   as follows:

.vb
            1  2  0  |  0  3  0  |  0  4
    Proc0   0  5  6  |  7  0  0  |  8  0
            9  0 10  | 11  0  0  | 12  0
    -------------------------------------
           13  0 14  | 15 16 17  |  0  0
    Proc1   0 18  0  | 19 20 21  |  0  0
            0  0  0  | 22 23  0  | 24  0
    -------------------------------------
    Proc2  25 26 27  |  0  0 28  | 29  0
           30  0  0  | 31 32 33  |  0 34
.ve

   This can be represented as a collection of submatrices as:

.vb
      A B C
      D E F
      G H I
.ve

   Where the submatrices A,B,C are owned by proc0, D,E,F are
   owned by proc1, G,H,I are owned by proc2.

   The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively.
   The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively.
   The 'M','N' parameters are 8,8, and have the same values on all procs.

   The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are
   submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices
   corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively.
   Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL
   part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ
   matrix, ans [DF] as another SeqAIJ matrix.

   When d_nz, o_nz parameters are specified, d_nz storage elements are
   allocated for every row of the local diagonal submatrix, and o_nz
   storage locations are allocated for every row of the OFF-DIAGONAL submat.
   One way to choose d_nz and o_nz is to use the max nonzerors per local
   rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices.
   In this case, the values of d_nz,o_nz are:
.vb
     proc0 : dnz = 2, o_nz = 2
     proc1 : dnz = 3, o_nz = 2
     proc2 : dnz = 1, o_nz = 4
.ve
   We are allocating m*(d_nz+o_nz) storage locations for every proc. This
   translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10
   for proc3. i.e we are using 12+15+10=37 storage locations to store
   34 values.

   When d_nnz, o_nnz parameters are specified, the storage is specified
   for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices.
   In the above case the values for d_nnz,o_nnz are:
.vb
     proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2]
     proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1]
     proc2: d_nnz = [1,1]   and o_nnz = [4,4]
.ve
   Here the space allocated is sum of all the above values i.e 34, and
   hence pre-allocation is perfect.

   Level: intermediate

.keywords: matrix, aij, compressed row, sparse, parallel

.seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(),
          MATMPIAIJ, MatGetInfo(), PetscSplitOwnership()
@*/
PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[])
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(B,MAT_CLASSID,1);
  PetscValidType(B,1);
  ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@
     MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard
         CSR format the local rows.

   Collective on MPI_Comm

   Input Parameters:
+  comm - MPI communicator
.  m - number of local rows (Cannot be PETSC_DECIDE)
.  n - This value should be the same as the local size used in creating the
       x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have
       calculated if N is given) For square matrices n is almost always m.
.  M - number of global rows (or PETSC_DETERMINE to have calculated if m is given)
.  N - number of global columns (or PETSC_DETERMINE to have calculated if n is given)
.   i - row indices
.   j - column indices
-   a - matrix values

   Output Parameter:
.   mat - the matrix

   Level: intermediate

   Notes:
       The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc;
     thus you CANNOT change the matrix entries by changing the values of a[] after you have
     called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays.

       The i and j indices are 0 based, and i indices are indices corresponding to the local j array.

       The format which is used for the sparse matrix input, is equivalent to a
    row-major ordering.. i.e for the following matrix, the input data expected is
    as shown

$        1 0 0
$        2 0 3     P0
$       -------
$        4 5 6     P1
$
$     Process0 [P0]: rows_owned=[0,1]
$        i =  {0,1,3}  [size = nrow+1  = 2+1]
$        j =  {0,0,2}  [size = 3]
$        v =  {1,2,3}  [size = 3]
$
$     Process1 [P1]: rows_owned=[2]
$        i =  {0,3}    [size = nrow+1  = 1+1]
$        j =  {0,1,2}  [size = 3]
$        v =  {4,5,6}  [size = 3]

.keywords: matrix, aij, compressed row, sparse, parallel

.seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(),
          MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays()
@*/
PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0");
  if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative");
  ierr = MatCreate(comm,mat);CHKERRQ(ierr);
  ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr);
  /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */
  ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr);
  ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
   MatCreateAIJ - Creates a sparse parallel matrix in AIJ format
   (the default parallel PETSc format).  For good matrix assembly performance
   the user should preallocate the matrix storage by setting the parameters
   d_nz (or d_nnz) and o_nz (or o_nnz).  By setting these parameters accurately,
   performance can be increased by more than a factor of 50.

   Collective on MPI_Comm

   Input Parameters:
+  comm - MPI communicator
.  m - number of local rows (or PETSC_DECIDE to have calculated if M is given)
           This value should be the same as the local size used in creating the
           y vector for the matrix-vector product y = Ax.
.  n - This value should be the same as the local size used in creating the
       x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have
       calculated if N is given) For square matrices n is almost always m.
.  M - number of global rows (or PETSC_DETERMINE to have calculated if m is given)
.  N - number of global columns (or PETSC_DETERMINE to have calculated if n is given)
.  d_nz  - number of nonzeros per row in DIAGONAL portion of local submatrix
           (same value is used for all local rows)
.  d_nnz - array containing the number of nonzeros in the various rows of the
           DIAGONAL portion of the local submatrix (possibly different for each row)
           or NULL, if d_nz is used to specify the nonzero structure.
           The size of this array is equal to the number of local rows, i.e 'm'.
.  o_nz  - number of nonzeros per row in the OFF-DIAGONAL portion of local
           submatrix (same value is used for all local rows).
-  o_nnz - array containing the number of nonzeros in the various rows of the
           OFF-DIAGONAL portion of the local submatrix (possibly different for
           each row) or NULL, if o_nz is used to specify the nonzero
           structure. The size of this array is equal to the number
           of local rows, i.e 'm'.

   Output Parameter:
.  A - the matrix

   It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(),
   MatXXXXSetPreallocation() paradgm instead of this routine directly.
   [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation]

   Notes:
   If the *_nnz parameter is given then the *_nz parameter is ignored

   m,n,M,N parameters specify the size of the matrix, and its partitioning across
   processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate
   storage requirements for this matrix.

   If PETSC_DECIDE or  PETSC_DETERMINE is used for a particular argument on one
   processor than it must be used on all processors that share the object for
   that argument.

   The user MUST specify either the local or global matrix dimensions
   (possibly both).

   The parallel matrix is partitioned across processors such that the
   first m0 rows belong to process 0, the next m1 rows belong to
   process 1, the next m2 rows belong to process 2 etc.. where
   m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores
   values corresponding to [m x N] submatrix.

   The columns are logically partitioned with the n0 columns belonging
   to 0th partition, the next n1 columns belonging to the next
   partition etc.. where n0,n1,n2... are the input parameter 'n'.

   The DIAGONAL portion of the local submatrix on any given processor
   is the submatrix corresponding to the rows and columns m,n
   corresponding to the given processor. i.e diagonal matrix on
   process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1]
   etc. The remaining portion of the local submatrix [m x (N-n)]
   constitute the OFF-DIAGONAL portion. The example below better
   illustrates this concept.

   For a square global matrix we define each processor's diagonal portion
   to be its local rows and the corresponding columns (a square submatrix);
   each processor's off-diagonal portion encompasses the remainder of the
   local matrix (a rectangular submatrix).

   If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored.

   When calling this routine with a single process communicator, a matrix of
   type SEQAIJ is returned.  If a matrix of type MATMPIAIJ is desired for this
   type of communicator, use the construction mechanism:
     MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...);

   By default, this format uses inodes (identical nodes) when possible.
   We search for consecutive rows with the same nonzero structure, thereby
   reusing matrix information to achieve increased efficiency.

   Options Database Keys:
+  -mat_no_inode  - Do not use inodes
.  -mat_inode_limit <limit> - Sets inode limit (max limit=5)
-  -mat_aij_oneindex - Internally use indexing starting at 1
        rather than 0.  Note that when calling MatSetValues(),
        the user still MUST index entries starting at 0!


   Example usage:

   Consider the following 8x8 matrix with 34 non-zero values, that is
   assembled across 3 processors. Lets assume that proc0 owns 3 rows,
   proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown
   as follows:

.vb
            1  2  0  |  0  3  0  |  0  4
    Proc0   0  5  6  |  7  0  0  |  8  0
            9  0 10  | 11  0  0  | 12  0
    -------------------------------------
           13  0 14  | 15 16 17  |  0  0
    Proc1   0 18  0  | 19 20 21  |  0  0
            0  0  0  | 22 23  0  | 24  0
    -------------------------------------
    Proc2  25 26 27  |  0  0 28  | 29  0
           30  0  0  | 31 32 33  |  0 34
.ve

   This can be represented as a collection of submatrices as:

.vb
      A B C
      D E F
      G H I
.ve

   Where the submatrices A,B,C are owned by proc0, D,E,F are
   owned by proc1, G,H,I are owned by proc2.

   The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively.
   The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively.
   The 'M','N' parameters are 8,8, and have the same values on all procs.

   The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are
   submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices
   corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively.
   Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL
   part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ
   matrix, ans [DF] as another SeqAIJ matrix.

   When d_nz, o_nz parameters are specified, d_nz storage elements are
   allocated for every row of the local diagonal submatrix, and o_nz
   storage locations are allocated for every row of the OFF-DIAGONAL submat.
   One way to choose d_nz and o_nz is to use the max nonzerors per local
   rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices.
   In this case, the values of d_nz,o_nz are:
.vb
     proc0 : dnz = 2, o_nz = 2
     proc1 : dnz = 3, o_nz = 2
     proc2 : dnz = 1, o_nz = 4
.ve
   We are allocating m*(d_nz+o_nz) storage locations for every proc. This
   translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10
   for proc3. i.e we are using 12+15+10=37 storage locations to store
   34 values.

   When d_nnz, o_nnz parameters are specified, the storage is specified
   for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices.
   In the above case the values for d_nnz,o_nnz are:
.vb
     proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2]
     proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1]
     proc2: d_nnz = [1,1]   and o_nnz = [4,4]
.ve
   Here the space allocated is sum of all the above values i.e 34, and
   hence pre-allocation is perfect.

   Level: intermediate

.keywords: matrix, aij, compressed row, sparse, parallel

.seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(),
          MATMPIAIJ, MatCreateMPIAIJWithArrays()
@*/
PetscErrorCode  MatCreateAIJ(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[],Mat *A)
{
  PetscErrorCode ierr;
  PetscMPIInt    size;

  PetscFunctionBegin;
  ierr = MatCreate(comm,A);CHKERRQ(ierr);
  ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  if (size > 1) {
    ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr);
    ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr);
  } else {
    ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr);
    ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[])
{
  Mat_MPIAIJ     *a = (Mat_MPIAIJ*)A->data;
  PetscBool      flg;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr);
  if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input");
  if (Ad)     *Ad     = a->A;
  if (Ao)     *Ao     = a->B;
  if (colmap) *colmap = a->garray;
  PetscFunctionReturn(0);
}

PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat)
{
  PetscErrorCode ierr;
  PetscInt       m,N,i,rstart,nnz,Ii;
  PetscInt       *indx;
  PetscScalar    *values;

  PetscFunctionBegin;
  ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr);
  if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */
    PetscInt       *dnz,*onz,sum,bs,cbs;

    if (n == PETSC_DECIDE) {
      ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr);
    }
    /* Check sum(n) = N */
    ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr);
    if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N);

    ierr    = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr);
    rstart -= m;

    ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr);
    for (i=0; i<m; i++) {
      ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr);
      ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr);
      ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr);
    }

    ierr = MatCreate(comm,outmat);CHKERRQ(ierr);
    ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
    ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr);
    ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr);
    ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr);
    ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr);
    ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr);
    ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);
  }

  /* numeric phase */
  ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr);
  for (i=0; i<m; i++) {
    ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr);
    Ii   = i + rstart;
    ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr);
    ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr);
  }
  ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatFileSplit(Mat A,char *outfile)
{
  PetscErrorCode    ierr;
  PetscMPIInt       rank;
  PetscInt          m,N,i,rstart,nnz;
  size_t            len;
  const PetscInt    *indx;
  PetscViewer       out;
  char              *name;
  Mat               B;
  const PetscScalar *values;

  PetscFunctionBegin;
  ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr);
  ierr = MatGetSize(A,0,&N);CHKERRQ(ierr);
  /* Should this be the type of the diagonal block of A? */
  ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr);
  ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr);
  ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr);
  ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr);
  ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr);
  ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr);
  for (i=0; i<m; i++) {
    ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr);
    ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr);
    ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr);
  }
  ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr);
  ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr);
  ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr);
  sprintf(name,"%s.%d",outfile,rank);
  ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr);
  ierr = PetscFree(name);CHKERRQ(ierr);
  ierr = MatView(B,out);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&out);CHKERRQ(ierr);
  ierr = MatDestroy(&B);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A)
{
  PetscErrorCode      ierr;
  Mat_Merge_SeqsToMPI *merge;
  PetscContainer      container;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr);
  if (container) {
    ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr);
    ierr = PetscFree(merge->id_r);CHKERRQ(ierr);
    ierr = PetscFree(merge->len_s);CHKERRQ(ierr);
    ierr = PetscFree(merge->len_r);CHKERRQ(ierr);
    ierr = PetscFree(merge->bi);CHKERRQ(ierr);
    ierr = PetscFree(merge->bj);CHKERRQ(ierr);
    ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr);
    ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr);
    ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr);
    ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr);
    ierr = PetscFree(merge->coi);CHKERRQ(ierr);
    ierr = PetscFree(merge->coj);CHKERRQ(ierr);
    ierr = PetscFree(merge->owners_co);CHKERRQ(ierr);
    ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr);
    ierr = PetscFree(merge);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr);
  }
  ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#include <../src/mat/utils/freespace.h>
#include <petscbt.h>

PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat)
{
  PetscErrorCode      ierr;
  MPI_Comm            comm;
  Mat_SeqAIJ          *a  =(Mat_SeqAIJ*)seqmat->data;
  PetscMPIInt         size,rank,taga,*len_s;
  PetscInt            N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj;
  PetscInt            proc,m;
  PetscInt            **buf_ri,**buf_rj;
  PetscInt            k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj;
  PetscInt            nrows,**buf_ri_k,**nextrow,**nextai;
  MPI_Request         *s_waits,*r_waits;
  MPI_Status          *status;
  MatScalar           *aa=a->a;
  MatScalar           **abuf_r,*ba_i;
  Mat_Merge_SeqsToMPI *merge;
  PetscContainer      container;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr);
  ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr);

  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);

  ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr);
  ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr);

  bi     = merge->bi;
  bj     = merge->bj;
  buf_ri = merge->buf_ri;
  buf_rj = merge->buf_rj;

  ierr   = PetscMalloc1(size,&status);CHKERRQ(ierr);
  owners = merge->rowmap->range;
  len_s  = merge->len_s;

  /* send and recv matrix values */
  /*-----------------------------*/
  ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr);
  ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr);

  ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr);
  for (proc=0,k=0; proc<size; proc++) {
    if (!len_s[proc]) continue;
    i    = owners[proc];
    ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr);
    k++;
  }

  if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);}
  if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);}
  ierr = PetscFree(status);CHKERRQ(ierr);

  ierr = PetscFree(s_waits);CHKERRQ(ierr);
  ierr = PetscFree(r_waits);CHKERRQ(ierr);

  /* insert mat values of mpimat */
  /*----------------------------*/
  ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr);
  ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr);

  for (k=0; k<merge->nrecv; k++) {
    buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */
    nrows       = *(buf_ri_k[k]);
    nextrow[k]  = buf_ri_k[k]+1;  /* next row number of k-th recved i-structure */
    nextai[k]   = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure  */
  }

  /* set values of ba */
  m = merge->rowmap->n;
  for (i=0; i<m; i++) {
    arow = owners[rank] + i;
    bj_i = bj+bi[i];  /* col indices of the i-th row of mpimat */
    bnzi = bi[i+1] - bi[i];
    ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr);

    /* add local non-zero vals of this proc's seqmat into ba */
    anzi   = ai[arow+1] - ai[arow];
    aj     = a->j + ai[arow];
    aa     = a->a + ai[arow];
    nextaj = 0;
    for (j=0; nextaj<anzi; j++) {
      if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */
        ba_i[j] += aa[nextaj++];
      }
    }

    /* add received vals into ba */
    for (k=0; k<merge->nrecv; k++) { /* k-th received message */
      /* i-th row */
      if (i == *nextrow[k]) {
        anzi   = *(nextai[k]+1) - *nextai[k];
        aj     = buf_rj[k] + *(nextai[k]);
        aa     = abuf_r[k] + *(nextai[k]);
        nextaj = 0;
        for (j=0; nextaj<anzi; j++) {
          if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */
            ba_i[j] += aa[nextaj++];
          }
        }
        nextrow[k]++; nextai[k]++;
      }
    }
    ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr);
  }
  ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr);
  ierr = PetscFree(abuf_r);CHKERRQ(ierr);
  ierr = PetscFree(ba_i);CHKERRQ(ierr);
  ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr);
  ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode  MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat)
{
  PetscErrorCode      ierr;
  Mat                 B_mpi;
  Mat_SeqAIJ          *a=(Mat_SeqAIJ*)seqmat->data;
  PetscMPIInt         size,rank,tagi,tagj,*len_s,*len_si,*len_ri;
  PetscInt            **buf_rj,**buf_ri,**buf_ri_k;
  PetscInt            M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j;
  PetscInt            len,proc,*dnz,*onz,bs,cbs;
  PetscInt            k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0;
  PetscInt            nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai;
  MPI_Request         *si_waits,*sj_waits,*ri_waits,*rj_waits;
  MPI_Status          *status;
  PetscFreeSpaceList  free_space=NULL,current_space=NULL;
  PetscBT             lnkbt;
  Mat_Merge_SeqsToMPI *merge;
  PetscContainer      container;

  PetscFunctionBegin;
  ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr);

  /* make sure it is a PETSc comm */
  ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);

  ierr = PetscNew(&merge);CHKERRQ(ierr);
  ierr = PetscMalloc1(size,&status);CHKERRQ(ierr);

  /* determine row ownership */
  /*---------------------------------------------------------*/
  ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr);
  ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr);
  ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr);
  ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr);
  ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr);
  ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr);
  ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr);

  m      = merge->rowmap->n;
  owners = merge->rowmap->range;

  /* determine the number of messages to send, their lengths */
  /*---------------------------------------------------------*/
  len_s = merge->len_s;

  len          = 0; /* length of buf_si[] */
  merge->nsend = 0;
  for (proc=0; proc<size; proc++) {
    len_si[proc] = 0;
    if (proc == rank) {
      len_s[proc] = 0;
    } else {
      len_si[proc] = owners[proc+1] - owners[proc] + 1;
      len_s[proc]  = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */
    }
    if (len_s[proc]) {
      merge->nsend++;
      nrows = 0;
      for (i=owners[proc]; i<owners[proc+1]; i++) {
        if (ai[i+1] > ai[i]) nrows++;
      }
      len_si[proc] = 2*(nrows+1);
      len         += len_si[proc];
    }
  }

  /* determine the number and length of messages to receive for ij-structure */
  /*-------------------------------------------------------------------------*/
  ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr);
  ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr);

  /* post the Irecv of j-structure */
  /*-------------------------------*/
  ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr);
  ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr);

  /* post the Isend of j-structure */
  /*--------------------------------*/
  ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr);

  for (proc=0, k=0; proc<size; proc++) {
    if (!len_s[proc]) continue;
    i    = owners[proc];
    ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr);
    k++;
  }

  /* receives and sends of j-structure are complete */
  /*------------------------------------------------*/
  if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);}
  if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);}

  /* send and recv i-structure */
  /*---------------------------*/
  ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr);
  ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr);

  ierr   = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr);
  buf_si = buf_s;  /* points to the beginning of k-th msg to be sent */
  for (proc=0,k=0; proc<size; proc++) {
    if (!len_s[proc]) continue;
    /* form outgoing message for i-structure:
         buf_si[0]:                 nrows to be sent
               [1:nrows]:           row index (global)
               [nrows+1:2*nrows+1]: i-structure index
    */
    /*-------------------------------------------*/
    nrows       = len_si[proc]/2 - 1;
    buf_si_i    = buf_si + nrows+1;
    buf_si[0]   = nrows;
    buf_si_i[0] = 0;
    nrows       = 0;
    for (i=owners[proc]; i<owners[proc+1]; i++) {
      anzi = ai[i+1] - ai[i];
      if (anzi) {
        buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */
        buf_si[nrows+1]   = i-owners[proc]; /* local row index */
        nrows++;
      }
    }
    ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr);
    k++;
    buf_si += len_si[proc];
  }

  if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);}
  if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);}

  ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr);
  for (i=0; i<merge->nrecv; i++) {
    ierr = PetscInfo3(seqmat,"recv len_ri=%D, len_rj=%D from [%D]\n",len_ri[i],merge->len_r[i],merge->id_r[i]);CHKERRQ(ierr);
  }

  ierr = PetscFree(len_si);CHKERRQ(ierr);
  ierr = PetscFree(len_ri);CHKERRQ(ierr);
  ierr = PetscFree(rj_waits);CHKERRQ(ierr);
  ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr);
  ierr = PetscFree(ri_waits);CHKERRQ(ierr);
  ierr = PetscFree(buf_s);CHKERRQ(ierr);
  ierr = PetscFree(status);CHKERRQ(ierr);

  /* compute a local seq matrix in each processor */
  /*----------------------------------------------*/
  /* allocate bi array and free space for accumulating nonzero column info */
  ierr  = PetscMalloc1(m+1,&bi);CHKERRQ(ierr);
  bi[0] = 0;

  /* create and initialize a linked list */
  nlnk = N+1;
  ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr);

  /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */
  len  = ai[owners[rank+1]] - ai[owners[rank]];
  ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr);

  current_space = free_space;

  /* determine symbolic info for each local row */
  ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr);

  for (k=0; k<merge->nrecv; k++) {
    buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */
    nrows       = *buf_ri_k[k];
    nextrow[k]  = buf_ri_k[k] + 1;  /* next row number of k-th recved i-structure */
    nextai[k]   = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure  */
  }

  ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr);
  len  = 0;
  for (i=0; i<m; i++) {
    bnzi = 0;
    /* add local non-zero cols of this proc's seqmat into lnk */
    arow  = owners[rank] + i;
    anzi  = ai[arow+1] - ai[arow];
    aj    = a->j + ai[arow];
    ierr  = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr);
    bnzi += nlnk;
    /* add received col data into lnk */
    for (k=0; k<merge->nrecv; k++) { /* k-th received message */
      if (i == *nextrow[k]) { /* i-th row */
        anzi  = *(nextai[k]+1) - *nextai[k];
        aj    = buf_rj[k] + *nextai[k];
        ierr  = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr);
        bnzi += nlnk;
        nextrow[k]++; nextai[k]++;
      }
    }
    if (len < bnzi) len = bnzi;  /* =max(bnzi) */

    /* if free space is not available, make more free space */
    if (current_space->local_remaining<bnzi) {
      ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),&current_space);CHKERRQ(ierr);
      nspacedouble++;
    }
    /* copy data into free space, then initialize lnk */
    ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr);
    ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr);

    current_space->array           += bnzi;
    current_space->local_used      += bnzi;
    current_space->local_remaining -= bnzi;

    bi[i+1] = bi[i] + bnzi;
  }

  ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr);

  ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr);
  ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr);
  ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr);

  /* create symbolic parallel matrix B_mpi */
  /*---------------------------------------*/
  ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr);
  ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr);
  if (n==PETSC_DECIDE) {
    ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr);
  } else {
    ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
  }
  ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr);
  ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr);
  ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr);
  ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);
  ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);

  /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */
  B_mpi->assembled    = PETSC_FALSE;
  B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI;
  merge->bi           = bi;
  merge->bj           = bj;
  merge->buf_ri       = buf_ri;
  merge->buf_rj       = buf_rj;
  merge->coi          = NULL;
  merge->coj          = NULL;
  merge->owners_co    = NULL;

  ierr = PetscCommDestroy(&comm);CHKERRQ(ierr);

  /* attach the supporting struct to B_mpi for reuse */
  ierr    = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr);
  ierr    = PetscContainerSetPointer(container,merge);CHKERRQ(ierr);
  ierr    = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr);
  ierr    = PetscContainerDestroy(&container);CHKERRQ(ierr);
  *mpimat = B_mpi;

  ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
      MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential
                 matrices from each processor

    Collective on MPI_Comm

   Input Parameters:
+    comm - the communicators the parallel matrix will live on
.    seqmat - the input sequential matrices
.    m - number of local rows (or PETSC_DECIDE)
.    n - number of local columns (or PETSC_DECIDE)
-    scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX

   Output Parameter:
.    mpimat - the parallel matrix generated

    Level: advanced

   Notes:
     The dimensions of the sequential matrix in each processor MUST be the same.
     The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be
     destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat.
@*/
PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat)
{
  PetscErrorCode ierr;
  PetscMPIInt    size;

  PetscFunctionBegin;
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  if (size == 1) {
    ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr);
    if (scall == MAT_INITIAL_MATRIX) {
      ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr);
    } else {
      ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
    }
    ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr);
    PetscFunctionReturn(0);
  }
  ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr);
  if (scall == MAT_INITIAL_MATRIX) {
    ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr);
  }
  ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr);
  ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@
     MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential vector with
          mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained
          with MatGetSize()

    Not Collective

   Input Parameters:
+    A - the matrix
.    scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX

   Output Parameter:
.    A_loc - the local sequential matrix generated

    Level: developer

.seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed()

@*/
PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc)
{
  PetscErrorCode ierr;
  Mat_MPIAIJ     *mpimat=(Mat_MPIAIJ*)A->data;
  Mat_SeqAIJ     *mat,*a,*b;
  PetscInt       *ai,*aj,*bi,*bj,*cmap=mpimat->garray;
  MatScalar      *aa,*ba,*cam;
  PetscScalar    *ca;
  PetscInt       am=A->rmap->n,i,j,k,cstart=A->cmap->rstart;
  PetscInt       *ci,*cj,col,ncols_d,ncols_o,jo;
  PetscBool      match;
  MPI_Comm       comm;
  PetscMPIInt    size;

  PetscFunctionBegin;
  ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr);
  if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input");
  ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0);

  ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr);
  a = (Mat_SeqAIJ*)(mpimat->A)->data;
  b = (Mat_SeqAIJ*)(mpimat->B)->data;
  ai = a->i; aj = a->j; bi = b->i; bj = b->j;
  aa = a->a; ba = b->a;
  if (scall == MAT_INITIAL_MATRIX) {
    if (size == 1) {
      ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr);
      PetscFunctionReturn(0);
    }

    ierr  = PetscMalloc1(1+am,&ci);CHKERRQ(ierr);
    ci[0] = 0;
    for (i=0; i<am; i++) {
      ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]);
    }
    ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr);
    ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr);
    k    = 0;
    for (i=0; i<am; i++) {
      ncols_o = bi[i+1] - bi[i];
      ncols_d = ai[i+1] - ai[i];
      /* off-diagonal portion of A */
      for (jo=0; jo<ncols_o; jo++) {
        col = cmap[*bj];
        if (col >= cstart) break;
        cj[k]   = col; bj++;
        ca[k++] = *ba++;
      }
      /* diagonal portion of A */
      for (j=0; j<ncols_d; j++) {
        cj[k]   = cstart + *aj++;
        ca[k++] = *aa++;
      }
      /* off-diagonal portion of A */
      for (j=jo; j<ncols_o; j++) {
        cj[k]   = cmap[*bj++];
        ca[k++] = *ba++;
      }
    }
    /* put together the new matrix */
    ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr);
    /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */
    /* Since these are PETSc arrays, change flags to free them as necessary. */
    mat          = (Mat_SeqAIJ*)(*A_loc)->data;
    mat->free_a  = PETSC_TRUE;
    mat->free_ij = PETSC_TRUE;
    mat->nonew   = 0;
  } else if (scall == MAT_REUSE_MATRIX) {
    mat=(Mat_SeqAIJ*)(*A_loc)->data;
    ci = mat->i; cj = mat->j; cam = mat->a;
    for (i=0; i<am; i++) {
      /* off-diagonal portion of A */
      ncols_o = bi[i+1] - bi[i];
      for (jo=0; jo<ncols_o; jo++) {
        col = cmap[*bj];
        if (col >= cstart) break;
        *cam++ = *ba++; bj++;
      }
      /* diagonal portion of A */
      ncols_d = ai[i+1] - ai[i];
      for (j=0; j<ncols_d; j++) *cam++ = *aa++;
      /* off-diagonal portion of A */
      for (j=jo; j<ncols_o; j++) {
        *cam++ = *ba++; bj++;
      }
    }
  } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall);
  ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
     MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns

    Not Collective

   Input Parameters:
+    A - the matrix
.    scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX
-    row, col - index sets of rows and columns to extract (or NULL)

   Output Parameter:
.    A_loc - the local sequential matrix generated

    Level: developer

.seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat()

@*/
PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc)
{
  Mat_MPIAIJ     *a=(Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;
  PetscInt       i,start,end,ncols,nzA,nzB,*cmap,imark,*idx;
  IS             isrowa,iscola;
  Mat            *aloc;
  PetscBool      match;

  PetscFunctionBegin;
  ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr);
  if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input");
  ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr);
  if (!row) {
    start = A->rmap->rstart; end = A->rmap->rend;
    ierr  = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr);
  } else {
    isrowa = *row;
  }
  if (!col) {
    start = A->cmap->rstart;
    cmap  = a->garray;
    nzA   = a->A->cmap->n;
    nzB   = a->B->cmap->n;
    ierr  = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr);
    ncols = 0;
    for (i=0; i<nzB; i++) {
      if (cmap[i] < start) idx[ncols++] = cmap[i];
      else break;
    }
    imark = i;
    for (i=0; i<nzA; i++) idx[ncols++] = start + i;
    for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i];
    ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr);
  } else {
    iscola = *col;
  }
  if (scall != MAT_INITIAL_MATRIX) {
    ierr    = PetscMalloc1(1,&aloc);CHKERRQ(ierr);
    aloc[0] = *A_loc;
  }
  ierr   = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr);
  *A_loc = aloc[0];
  ierr   = PetscFree(aloc);CHKERRQ(ierr);
  if (!row) {
    ierr = ISDestroy(&isrowa);CHKERRQ(ierr);
  }
  if (!col) {
    ierr = ISDestroy(&iscola);CHKERRQ(ierr);
  }
  ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
    MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A

    Collective on Mat

   Input Parameters:
+    A,B - the matrices in mpiaij format
.    scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX
-    rowb, colb - index sets of rows and columns of B to extract (or NULL)

   Output Parameter:
+    rowb, colb - index sets of rows and columns of B to extract
-    B_seq - the sequential matrix generated

    Level: developer

@*/
PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq)
{
  Mat_MPIAIJ     *a=(Mat_MPIAIJ*)A->data;
  PetscErrorCode ierr;
  PetscInt       *idx,i,start,ncols,nzA,nzB,*cmap,imark;
  IS             isrowb,iscolb;
  Mat            *bseq=NULL;

  PetscFunctionBegin;
  if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) {
    SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%D, %D) != (%D,%D)",A->cmap->rstart,A->cmap->rend,B->rmap->rstart,B->rmap->rend);
  }
  ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr);

  if (scall == MAT_INITIAL_MATRIX) {
    start = A->cmap->rstart;
    cmap  = a->garray;
    nzA   = a->A->cmap->n;
    nzB   = a->B->cmap->n;
    ierr  = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr);
    ncols = 0;
    for (i=0; i<nzB; i++) {  /* row < local row index */
      if (cmap[i] < start) idx[ncols++] = cmap[i];
      else break;
    }
    imark = i;
    for (i=0; i<nzA; i++) idx[ncols++] = start + i;  /* local rows */
    for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */
    ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr);
    ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr);
  } else {
    if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX");
    isrowb  = *rowb; iscolb = *colb;
    ierr    = PetscMalloc1(1,&bseq);CHKERRQ(ierr);
    bseq[0] = *B_seq;
  }
  ierr   = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr);
  *B_seq = bseq[0];
  ierr   = PetscFree(bseq);CHKERRQ(ierr);
  if (!rowb) {
    ierr = ISDestroy(&isrowb);CHKERRQ(ierr);
  } else {
    *rowb = isrowb;
  }
  if (!colb) {
    ierr = ISDestroy(&iscolb);CHKERRQ(ierr);
  } else {
    *colb = iscolb;
  }
  ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
    MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns
    of the OFF-DIAGONAL portion of local A

    Collective on Mat

   Input Parameters:
+    A,B - the matrices in mpiaij format
-    scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX

   Output Parameter:
+    startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL)
.    startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL)
.    bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL)
-    B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N

    Level: developer

*/
PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth)
{
  VecScatter_MPI_General *gen_to,*gen_from;
  PetscErrorCode         ierr;
  Mat_MPIAIJ             *a=(Mat_MPIAIJ*)A->data;
  Mat_SeqAIJ             *b_oth;
  VecScatter             ctx =a->Mvctx;
  MPI_Comm               comm;
  PetscMPIInt            *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank;
  PetscInt               *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj;
  PetscInt               *rvalues,*svalues;
  MatScalar              *b_otha,*bufa,*bufA;
  PetscInt               i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len;
  MPI_Request            *rwaits = NULL,*swaits = NULL;
  MPI_Status             *sstatus,rstatus;
  PetscMPIInt            jj,size;
  PetscInt               *cols,sbs,rbs;
  PetscScalar            *vals;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);

  if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) {
    SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%d, %d) != (%d,%d)",A->cmap->rstart,A->cmap->rend,B->rmap->rstart,B->rmap->rend);
  }
  ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);

  if (size == 1) {
    startsj_s = NULL;
    bufa_ptr  = NULL;
    *B_oth    = NULL;
    PetscFunctionReturn(0);
  }

  gen_to   = (VecScatter_MPI_General*)ctx->todata;
  gen_from = (VecScatter_MPI_General*)ctx->fromdata;
  nrecvs   = gen_from->n;
  nsends   = gen_to->n;

  ierr    = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr);
  srow    = gen_to->indices;    /* local row index to be sent */
  sstarts = gen_to->starts;
  sprocs  = gen_to->procs;
  sstatus = gen_to->sstatus;
  sbs     = gen_to->bs;
  rstarts = gen_from->starts;
  rprocs  = gen_from->procs;
  rbs     = gen_from->bs;

  if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX;
  if (scall == MAT_INITIAL_MATRIX) {
    /* i-array */
    /*---------*/
    /*  post receives */
    ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr);
    for (i=0; i<nrecvs; i++) {
      rowlen = rvalues + rstarts[i]*rbs;
      nrows  = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */
      ierr   = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr);
    }

    /* pack the outgoing message */
    ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr);

    sstartsj[0] = 0;
    rstartsj[0] = 0;
    len         = 0; /* total length of j or a array to be sent */
    k           = 0;
    ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr);
    for (i=0; i<nsends; i++) {
      rowlen = svalues + sstarts[i]*sbs;
      nrows  = sstarts[i+1]-sstarts[i]; /* num of block rows */
      for (j=0; j<nrows; j++) {
        row = srow[k] + B->rmap->range[rank]; /* global row idx */
        for (l=0; l<sbs; l++) {
          ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */

          rowlen[j*sbs+l] = ncols;

          len += ncols;
          ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr);
        }
        k++;
      }
      ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr);

      sstartsj[i+1] = len;  /* starting point of (i+1)-th outgoing msg in bufj and bufa */
    }
    /* recvs and sends of i-array are completed */
    i = nrecvs;
    while (i--) {
      ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr);
    }
    if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);}
    ierr = PetscFree(svalues);CHKERRQ(ierr);

    /* allocate buffers for sending j and a arrays */
    ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr);
    ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr);

    /* create i-array of B_oth */
    ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr);

    b_othi[0] = 0;
    len       = 0; /* total length of j or a array to be received */
    k         = 0;
    for (i=0; i<nrecvs; i++) {
      rowlen = rvalues + rstarts[i]*rbs;
      nrows  = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */
      for (j=0; j<nrows; j++) {
        b_othi[k+1] = b_othi[k] + rowlen[j];
        ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr);
        k++;
      }
      rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */
    }
    ierr = PetscFree(rvalues);CHKERRQ(ierr);

    /* allocate space for j and a arrrays of B_oth */
    ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr);
    ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr);

    /* j-array */
    /*---------*/
    /*  post receives of j-array */
    for (i=0; i<nrecvs; i++) {
      nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */
      ierr  = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr);
    }

    /* pack the outgoing message j-array */
    k = 0;
    for (i=0; i<nsends; i++) {
      nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */
      bufJ  = bufj+sstartsj[i];
      for (j=0; j<nrows; j++) {
        row = srow[k++] + B->rmap->range[rank];  /* global row idx */
        for (ll=0; ll<sbs; ll++) {
          ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr);
          for (l=0; l<ncols; l++) {
            *bufJ++ = cols[l];
          }
          ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr);
        }
      }
      ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr);
    }

    /* recvs and sends of j-array are completed */
    i = nrecvs;
    while (i--) {
      ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr);
    }
    if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);}
  } else if (scall == MAT_REUSE_MATRIX) {
    sstartsj = *startsj_s;
    rstartsj = *startsj_r;
    bufa     = *bufa_ptr;
    b_oth    = (Mat_SeqAIJ*)(*B_oth)->data;
    b_otha   = b_oth->a;
  } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container");

  /* a-array */
  /*---------*/
  /*  post receives of a-array */
  for (i=0; i<nrecvs; i++) {
    nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */
    ierr  = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr);
  }

  /* pack the outgoing message a-array */
  k = 0;
  for (i=0; i<nsends; i++) {
    nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */
    bufA  = bufa+sstartsj[i];
    for (j=0; j<nrows; j++) {
      row = srow[k++] + B->rmap->range[rank];  /* global row idx */
      for (ll=0; ll<sbs; ll++) {
        ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr);
        for (l=0; l<ncols; l++) {
          *bufA++ = vals[l];
        }
        ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr);
      }
    }
    ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr);
  }
  /* recvs and sends of a-array are completed */
  i = nrecvs;
  while (i--) {
    ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr);
  }
  if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);}
  ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr);

  if (scall == MAT_INITIAL_MATRIX) {
    /* put together the new matrix */
    ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr);

    /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */
    /* Since these are PETSc arrays, change flags to free them as necessary. */
    b_oth          = (Mat_SeqAIJ*)(*B_oth)->data;
    b_oth->free_a  = PETSC_TRUE;
    b_oth->free_ij = PETSC_TRUE;
    b_oth->nonew   = 0;

    ierr = PetscFree(bufj);CHKERRQ(ierr);
    if (!startsj_s || !bufa_ptr) {
      ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr);
      ierr = PetscFree(bufa_ptr);CHKERRQ(ierr);
    } else {
      *startsj_s = sstartsj;
      *startsj_r = rstartsj;
      *bufa_ptr  = bufa;
    }
  }
  ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
  MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication.

  Not Collective

  Input Parameters:
. A - The matrix in mpiaij format

  Output Parameter:
+ lvec - The local vector holding off-process values from the argument to a matrix-vector product
. colmap - A map from global column index to local index into lvec
- multScatter - A scatter from the argument of a matrix-vector product to lvec

  Level: developer

@*/
#if defined(PETSC_USE_CTABLE)
PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter)
#else
PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter)
#endif
{
  Mat_MPIAIJ *a;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(A, MAT_CLASSID, 1);
  PetscValidPointer(lvec, 2);
  PetscValidPointer(colmap, 3);
  PetscValidPointer(multScatter, 4);
  a = (Mat_MPIAIJ*) A->data;
  if (lvec) *lvec = a->lvec;
  if (colmap) *colmap = a->colmap;
  if (multScatter) *multScatter = a->Mvctx;
  PetscFunctionReturn(0);
}

PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*);
PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*);
PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*);
#if defined(PETSC_HAVE_ELEMENTAL)
PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*);
#endif
#if defined(PETSC_HAVE_HYPRE)
PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*);
PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*);
#endif
PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*);

/*
    Computes (B'*A')' since computing B*A directly is untenable

               n                       p                          p
        (              )       (              )         (                  )
      m (      A       )  *  n (       B      )   =   m (         C        )
        (              )       (              )         (                  )

*/
PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C)
{
  PetscErrorCode ierr;
  Mat            At,Bt,Ct;

  PetscFunctionBegin;
  ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr);
  ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr);
  ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr);
  ierr = MatDestroy(&At);CHKERRQ(ierr);
  ierr = MatDestroy(&Bt);CHKERRQ(ierr);
  ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr);
  ierr = MatDestroy(&Ct);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C)
{
  PetscErrorCode ierr;
  PetscInt       m=A->rmap->n,n=B->cmap->n;
  Mat            Cmat;

  PetscFunctionBegin;
  if (A->cmap->n != B->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"A->cmap->n %d != B->rmap->n %d\n",A->cmap->n,B->rmap->n);
  ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr);
  ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr);
  ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr);
  ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ;

  *C = Cmat;
  PetscFunctionReturn(0);
}

/* ----------------------------------------------------------------*/
PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (scall == MAT_INITIAL_MATRIX) {
    ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr);
    ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr);
    ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr);
  }
  ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr);
  ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr);
  ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*MC
   MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices.

   Options Database Keys:
. -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions()

  Level: beginner

.seealso: MatCreateAIJ()
M*/

PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B)
{
  Mat_MPIAIJ     *b;
  PetscErrorCode ierr;
  PetscMPIInt    size;

  PetscFunctionBegin;
  ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr);

  ierr          = PetscNewLog(B,&b);CHKERRQ(ierr);
  B->data       = (void*)b;
  ierr          = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr);
  B->assembled  = PETSC_FALSE;
  B->insertmode = NOT_SET_VALUES;
  b->size       = size;

  ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr);

  /* build cache for off array entries formed */
  ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr);

  b->donotstash  = PETSC_FALSE;
  b->colmap      = 0;
  b->garray      = 0;
  b->roworiented = PETSC_TRUE;

  /* stuff used for matrix vector multiply */
  b->lvec  = NULL;
  b->Mvctx = NULL;

  /* stuff for MatGetRow() */
  b->rowindices   = 0;
  b->rowvalues    = 0;
  b->getrowactive = PETSC_FALSE;

  /* flexible pointer used in CUSP/CUSPARSE classes */
  b->spptr = NULL;

  ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr);
#if defined(PETSC_HAVE_ELEMENTAL)
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr);
#endif
#if defined(PETSC_HAVE_HYPRE)
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr);
#endif
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr);
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr);
#if defined(PETSC_HAVE_HYPRE)
  ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr);
#endif
  ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*@C
     MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal"
         and "off-diagonal" part of the matrix in CSR format.

   Collective on MPI_Comm

   Input Parameters:
+  comm - MPI communicator
.  m - number of local rows (Cannot be PETSC_DECIDE)
.  n - This value should be the same as the local size used in creating the
       x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have
       calculated if N is given) For square matrices n is almost always m.
.  M - number of global rows (or PETSC_DETERMINE to have calculated if m is given)
.  N - number of global columns (or PETSC_DETERMINE to have calculated if n is given)
.   i - row indices for "diagonal" portion of matrix
.   j - column indices
.   a - matrix values
.   oi - row indices for "off-diagonal" portion of matrix
.   oj - column indices
-   oa - matrix values

   Output Parameter:
.   mat - the matrix

   Level: advanced

   Notes:
       The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user
       must free the arrays once the matrix has been destroyed and not before.

       The i and j indices are 0 based

       See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix

       This sets local rows and cannot be used to set off-processor values.

       Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a
       legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does
       not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because
       the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to
       keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all
       communication if it is known that only local entries will be set.

.keywords: matrix, aij, compressed row, sparse, parallel

.seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(),
          MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays()
@*/
PetscErrorCode MatCreateMPIAIJWithSplitArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,PetscInt i[],PetscInt j[],PetscScalar a[],PetscInt oi[], PetscInt oj[],PetscScalar oa[],Mat *mat)
{
  PetscErrorCode ierr;
  Mat_MPIAIJ     *maij;

  PetscFunctionBegin;
  if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative");
  if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0");
  if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0");
  ierr = MatCreate(comm,mat);CHKERRQ(ierr);
  ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr);
  ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr);
  maij = (Mat_MPIAIJ*) (*mat)->data;

  (*mat)->preallocated = PETSC_TRUE;

  ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr);
  ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr);

  ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr);
  ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr);

  ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr);
  ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
    Special version for direct calls from Fortran
*/
#include <petsc/private/fortranimpl.h>

/* Change these macros so can be used in void function */
#undef CHKERRQ
#define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr)
#undef SETERRQ2
#define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr)
#undef SETERRQ3
#define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr)
#undef SETERRQ
#define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr)

#if defined(PETSC_HAVE_FORTRAN_CAPS)
#define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ
#elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE)
#define matsetvaluesmpiaij_ matsetvaluesmpiaij
#else
#endif
PETSC_EXTERN void PETSC_STDCALL matsetvaluesmpiaij_(Mat *mmat,PetscInt *mm,const PetscInt im[],PetscInt *mn,const PetscInt in[],const PetscScalar v[],InsertMode *maddv,PetscErrorCode *_ierr)
{
  Mat            mat  = *mmat;
  PetscInt       m    = *mm, n = *mn;
  InsertMode     addv = *maddv;
  Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
  PetscScalar    value;
  PetscErrorCode ierr;

  MatCheckPreallocated(mat,1);
  if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv;

#if defined(PETSC_USE_DEBUG)
  else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values");
#endif
  {
    PetscInt  i,j,rstart  = mat->rmap->rstart,rend = mat->rmap->rend;
    PetscInt  cstart      = mat->cmap->rstart,cend = mat->cmap->rend,row,col;
    PetscBool roworiented = aij->roworiented;

    /* Some Variables required in the macro */
    Mat        A                 = aij->A;
    Mat_SeqAIJ *a                = (Mat_SeqAIJ*)A->data;
    PetscInt   *aimax            = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j;
    MatScalar  *aa               = a->a;
    PetscBool  ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE);
    Mat        B                 = aij->B;
    Mat_SeqAIJ *b                = (Mat_SeqAIJ*)B->data;
    PetscInt   *bimax            = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n;
    MatScalar  *ba               = b->a;

    PetscInt  *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2;
    PetscInt  nonew = a->nonew;
    MatScalar *ap1,*ap2;

    PetscFunctionBegin;
    for (i=0; i<m; i++) {
      if (im[i] < 0) continue;
#if defined(PETSC_USE_DEBUG)
      if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1);
#endif
      if (im[i] >= rstart && im[i] < rend) {
        row      = im[i] - rstart;
        lastcol1 = -1;
        rp1      = aj + ai[row];
        ap1      = aa + ai[row];
        rmax1    = aimax[row];
        nrow1    = ailen[row];
        low1     = 0;
        high1    = nrow1;
        lastcol2 = -1;
        rp2      = bj + bi[row];
        ap2      = ba + bi[row];
        rmax2    = bimax[row];
        nrow2    = bilen[row];
        low2     = 0;
        high2    = nrow2;

        for (j=0; j<n; j++) {
          if (roworiented) value = v[i*n+j];
          else value = v[i+j*m];
          if (in[j] >= cstart && in[j] < cend) {
            col = in[j] - cstart;
            if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue;
            MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]);
          } else if (in[j] < 0) continue;
#if defined(PETSC_USE_DEBUG)
          else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1);
#endif
          else {
            if (mat->was_assembled) {
              if (!aij->colmap) {
                ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr);
              }
#if defined(PETSC_USE_CTABLE)
              ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr);
              col--;
#else
              col = aij->colmap[in[j]] - 1;
#endif
              if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue;
              if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) {
                ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr);
                col  =  in[j];
                /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */
                B     = aij->B;
                b     = (Mat_SeqAIJ*)B->data;
                bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j;
                rp2   = bj + bi[row];
                ap2   = ba + bi[row];
                rmax2 = bimax[row];
                nrow2 = bilen[row];
                low2  = 0;
                high2 = nrow2;
                bm    = aij->B->rmap->n;
                ba    = b->a;
              }
            } else col = in[j];
            MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]);
          }
        }
      } else if (!aij->donotstash) {
        if (roworiented) {
          ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr);
        } else {
          ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr);
        }
      }
    }
  }
  PetscFunctionReturnVoid();
}