PetscErrorCode MatSetUpMultiply_MPIBAIJ(Mat mat)
{
Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data;
Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)(baij->B->data);
PetscErrorCode ierr;
PetscInt i,j,*aj = B->j,ec = 0,*garray;
PetscInt bs = mat->rmap->bs,*stmp;
IS from,to;
Vec gvec;
#if defined(PETSC_USE_CTABLE)
PetscTable gid1_lid1;
PetscTablePosition tpos;
PetscInt gid,lid;
#else
PetscInt Nbs = baij->Nbs,*indices;
#endif
PetscFunctionBegin;
#if defined(PETSC_USE_CTABLE)
/* use a table - Mark Adams */
ierr = PetscTableCreate(B->mbs,baij->Nbs+1,&gid1_lid1);CHKERRQ(ierr);
for (i=0; i<B->mbs; i++) {
for (j=0; j<B->ilen[i]; j++) {
PetscInt data,gid1 = aj[B->i[i]+j] + 1;
ierr = PetscTableFind(gid1_lid1,gid1,&data);CHKERRQ(ierr);
if (!data) {
/* one based table */
ierr = PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
/* form array of columns we need */
ierr = PetscMalloc((ec+1)*sizeof(PetscInt),&garray);CHKERRQ(ierr);
ierr = PetscTableGetHeadPosition(gid1_lid1,&tpos);CHKERRQ(ierr);
while (tpos) {
ierr = PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);CHKERRQ(ierr);
gid--; lid--;
garray[lid] = gid;
}
ierr = PetscSortInt(ec,garray);CHKERRQ(ierr);
ierr = PetscTableRemoveAll(gid1_lid1);CHKERRQ(ierr);
for (i=0; i<ec; i++) {
ierr = PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr);
}
/* compact out the extra columns in B */
for (i=0; i<B->mbs; i++) {
for (j=0; j<B->ilen[i]; j++) {
PetscInt gid1 = aj[B->i[i] + j] + 1;
ierr = PetscTableFind(gid1_lid1,gid1,&lid);CHKERRQ(ierr);
lid--;
aj[B->i[i]+j] = lid;
}
}
B->nbs = ec;
baij->B->cmap->n = baij->B->cmap->N = ec*mat->rmap->bs;
ierr = PetscLayoutSetUp((baij->B->cmap));CHKERRQ(ierr);
ierr = PetscTableDestroy(&gid1_lid1);CHKERRQ(ierr);
#else
/* Make an array as long as the number of columns */
/* mark those columns that are in baij->B */
ierr = PetscMalloc((Nbs+1)*sizeof(PetscInt),&indices);CHKERRQ(ierr);
ierr = PetscMemzero(indices,Nbs*sizeof(PetscInt));CHKERRQ(ierr);
for (i=0; i<B->mbs; i++) {
for (j=0; j<B->ilen[i]; j++) {
if (!indices[aj[B->i[i] + j]]) ec++;
indices[aj[B->i[i] + j]] = 1;
}
}
/* form array of columns we need */
ierr = PetscMalloc((ec+1)*sizeof(PetscInt),&garray);CHKERRQ(ierr);
ec = 0;
for (i=0; i<Nbs; i++) {
if (indices[i]) {
garray[ec++] = i;
}
}
/* make indices now point into garray */
for (i=0; i<ec; i++) {
indices[garray[i]] = i;
}
/* compact out the extra columns in B */
for (i=0; i<B->mbs; i++) {
for (j=0; j<B->ilen[i]; j++) {
aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
}
}
B->nbs = ec;
baij->B->cmap->n = baij->B->cmap->N = ec*mat->rmap->bs;
ierr = PetscLayoutSetUp((baij->B->cmap));CHKERRQ(ierr);
ierr = PetscFree(indices);CHKERRQ(ierr);
#endif
/* create local vector that is used to scatter into */
ierr = VecCreateSeq(PETSC_COMM_SELF,ec*bs,&baij->lvec);CHKERRQ(ierr);
/* create two temporary index sets for building scatter-gather */
ierr = ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);CHKERRQ(ierr);
ierr = PetscMalloc((ec+1)*sizeof(PetscInt),&stmp);CHKERRQ(ierr);
for (i=0; i<ec; i++) stmp[i] = i;
ierr = ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_OWN_POINTER,&to);CHKERRQ(ierr);
/* create temporary global vector to generate scatter context */
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);CHKERRQ(ierr);
ierr = VecScatterCreate(gvec,from,baij->lvec,to,&baij->Mvctx);CHKERRQ(ierr);
ierr = PetscLogObjectParent(mat,baij->Mvctx);CHKERRQ(ierr);
ierr = PetscLogObjectParent(mat,baij->lvec);CHKERRQ(ierr);
ierr = PetscLogObjectParent(mat,from);CHKERRQ(ierr);
ierr = PetscLogObjectParent(mat,to);CHKERRQ(ierr);
baij->garray = garray;
ierr = PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));CHKERRQ(ierr);
ierr = ISDestroy(&from);CHKERRQ(ierr);
ierr = ISDestroy(&to);CHKERRQ(ierr);
ierr = VecDestroy(&gvec);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatSetUpMultiply_MPIAIJ(Mat mat)
{
Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data;
Mat_SeqAIJ *B = (Mat_SeqAIJ*)(aij->B->data);
PetscErrorCode ierr;
PetscInt i,j,*aj = B->j,ec = 0,*garray;
IS from,to;
Vec gvec;
#if defined(PETSC_USE_CTABLE)
PetscTable gid1_lid1;
PetscTablePosition tpos;
PetscInt gid,lid;
#else
PetscInt N = mat->cmap->N,*indices;
#endif
PetscFunctionBegin;
if (!aij->garray) {
#if defined(PETSC_USE_CTABLE)
/* use a table */
ierr = PetscTableCreate(aij->B->rmap->n,mat->cmap->N+1,&gid1_lid1);CHKERRQ(ierr);
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
PetscInt data,gid1 = aj[B->i[i] + j] + 1;
ierr = PetscTableFind(gid1_lid1,gid1,&data);CHKERRQ(ierr);
if (!data) {
/* one based table */
ierr = PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
/* form array of columns we need */
ierr = PetscMalloc1(ec+1,&garray);CHKERRQ(ierr);
ierr = PetscTableGetHeadPosition(gid1_lid1,&tpos);CHKERRQ(ierr);
while (tpos) {
ierr = PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);CHKERRQ(ierr);
gid--;
lid--;
garray[lid] = gid;
}
ierr = PetscSortInt(ec,garray);CHKERRQ(ierr); /* sort, and rebuild */
ierr = PetscTableRemoveAll(gid1_lid1);CHKERRQ(ierr);
for (i=0; i<ec; i++) {
ierr = PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr);
}
/* compact out the extra columns in B */
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
PetscInt gid1 = aj[B->i[i] + j] + 1;
ierr = PetscTableFind(gid1_lid1,gid1,&lid);CHKERRQ(ierr);
lid--;
aj[B->i[i] + j] = lid;
}
}
aij->B->cmap->n = aij->B->cmap->N = ec;
aij->B->cmap->bs = 1;
ierr = PetscLayoutSetUp((aij->B->cmap));CHKERRQ(ierr);
ierr = PetscTableDestroy(&gid1_lid1);CHKERRQ(ierr);
#else
/* Make an array as long as the number of columns */
/* mark those columns that are in aij->B */
ierr = PetscCalloc1(N+1,&indices);CHKERRQ(ierr);
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
if (!indices[aj[B->i[i] + j]]) ec++;
indices[aj[B->i[i] + j]] = 1;
}
}
/* form array of columns we need */
ierr = PetscMalloc1(ec+1,&garray);CHKERRQ(ierr);
ec = 0;
for (i=0; i<N; i++) {
if (indices[i]) garray[ec++] = i;
}
/* make indices now point into garray */
for (i=0; i<ec; i++) {
indices[garray[i]] = i;
}
/* compact out the extra columns in B */
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
}
}
aij->B->cmap->n = aij->B->cmap->N = ec;
aij->B->cmap->bs = 1;
ierr = PetscLayoutSetUp((aij->B->cmap));CHKERRQ(ierr);
ierr = PetscFree(indices);CHKERRQ(ierr);
#endif
} else {
garray = aij->garray;
}
if (!aij->lvec) {
/* create local vector that is used to scatter into */
ierr = VecCreateSeq(PETSC_COMM_SELF,ec,&aij->lvec);CHKERRQ(ierr);
} else {
ierr = VecGetSize(aij->lvec,&ec);CHKERRQ(ierr);
}
/* create two temporary Index sets for build scatter gather */
ierr = ISCreateGeneral(((PetscObject)mat)->comm,ec,garray,PETSC_COPY_VALUES,&from);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,ec,0,1,&to);CHKERRQ(ierr);
/* create temporary global vector to generate scatter context */
/* This does not allocate the array's memory so is efficient */
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);CHKERRQ(ierr);
/* generate the scatter context */
if (aij->Mvctx_mpi1_flg) {
ierr = VecScatterDestroy(&aij->Mvctx_mpi1);CHKERRQ(ierr);
ierr = VecScatterCreate(gvec,from,aij->lvec,to,&aij->Mvctx_mpi1);CHKERRQ(ierr);
ierr = VecScatterSetType(aij->Mvctx_mpi1,VECSCATTERMPI1);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)aij->Mvctx_mpi1);CHKERRQ(ierr);
} else {
ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr);
ierr = VecScatterCreate(gvec,from,aij->lvec,to,&aij->Mvctx);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)aij->Mvctx);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)aij->lvec);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)mat,(ec+1)*sizeof(PetscInt));CHKERRQ(ierr);
}
aij->garray = garray;
ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)from);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)to);CHKERRQ(ierr);
ierr = ISDestroy(&from);CHKERRQ(ierr);
ierr = ISDestroy(&to);CHKERRQ(ierr);
ierr = VecDestroy(&gvec);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatFDColoringSetUp_MPIXAIJ(Mat mat,ISColoring iscoloring,MatFDColoring c)
{
PetscErrorCode ierr;
PetscMPIInt size,*ncolsonproc,*disp,nn;
PetscInt i,n,nrows,nrows_i,j,k,m,ncols,col,*rowhit,cstart,cend,colb;
const PetscInt *is,*A_ci,*A_cj,*B_ci,*B_cj,*row=NULL,*ltog=NULL;
PetscInt nis=iscoloring->n,nctot,*cols;
IS *isa;
ISLocalToGlobalMapping map=mat->cmap->mapping;
PetscInt ctype=c->ctype,*spidxA,*spidxB,nz,bs,bs2,spidx;
Mat A,B;
PetscScalar *A_val,*B_val,**valaddrhit;
MatEntry *Jentry;
MatEntry2 *Jentry2;
PetscBool isBAIJ;
PetscInt bcols=c->bcols;
#if defined(PETSC_USE_CTABLE)
PetscTable colmap=NULL;
#else
PetscInt *colmap=NULL; /* local col number of off-diag col */
#endif
PetscFunctionBegin;
if (ctype == IS_COLORING_GHOSTED) {
if (!map) SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_ARG_INCOMP,"When using ghosted differencing matrix must have local to global mapping provided with MatSetLocalToGlobalMapping");
ierr = ISLocalToGlobalMappingGetIndices(map,<og);CHKERRQ(ierr);
}
ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)mat,MATMPIBAIJ,&isBAIJ);CHKERRQ(ierr);
if (isBAIJ) {
Mat_MPIBAIJ *baij=(Mat_MPIBAIJ*)mat->data;
Mat_SeqBAIJ *spA,*spB;
A = baij->A; spA = (Mat_SeqBAIJ*)A->data; A_val = spA->a;
B = baij->B; spB = (Mat_SeqBAIJ*)B->data; B_val = spB->a;
nz = spA->nz + spB->nz; /* total nonzero entries of mat */
if (!baij->colmap) {
ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr);
colmap = baij->colmap;
}
ierr = MatGetColumnIJ_SeqBAIJ_Color(A,0,PETSC_FALSE,PETSC_FALSE,&ncols,&A_ci,&A_cj,&spidxA,NULL);CHKERRQ(ierr);
ierr = MatGetColumnIJ_SeqBAIJ_Color(B,0,PETSC_FALSE,PETSC_FALSE,&ncols,&B_ci,&B_cj,&spidxB,NULL);CHKERRQ(ierr);
if (ctype == IS_COLORING_GLOBAL && c->htype[0] == 'd') { /* create vscale for storing dx */
PetscInt *garray;
ierr = PetscMalloc1(B->cmap->n,&garray);CHKERRQ(ierr);
for (i=0; i<baij->B->cmap->n/bs; i++) {
for (j=0; j<bs; j++) {
garray[i*bs+j] = bs*baij->garray[i]+j;
}
}
ierr = VecCreateGhost(PetscObjectComm((PetscObject)mat),mat->cmap->n,PETSC_DETERMINE,B->cmap->n,garray,&c->vscale);CHKERRQ(ierr);
ierr = PetscFree(garray);CHKERRQ(ierr);
}
} else {
Mat_MPIAIJ *aij=(Mat_MPIAIJ*)mat->data;
Mat_SeqAIJ *spA,*spB;
A = aij->A; spA = (Mat_SeqAIJ*)A->data; A_val = spA->a;
B = aij->B; spB = (Mat_SeqAIJ*)B->data; B_val = spB->a;
nz = spA->nz + spB->nz; /* total nonzero entries of mat */
if (!aij->colmap) {
/* Allow access to data structures of local part of matrix
- creates aij->colmap which maps global column number to local number in part B */
ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr);
colmap = aij->colmap;
}
ierr = MatGetColumnIJ_SeqAIJ_Color(A,0,PETSC_FALSE,PETSC_FALSE,&ncols,&A_ci,&A_cj,&spidxA,NULL);CHKERRQ(ierr);
ierr = MatGetColumnIJ_SeqAIJ_Color(B,0,PETSC_FALSE,PETSC_FALSE,&ncols,&B_ci,&B_cj,&spidxB,NULL);CHKERRQ(ierr);
bs = 1; /* only bs=1 is supported for non MPIBAIJ matrix */
if (ctype == IS_COLORING_GLOBAL && c->htype[0] == 'd') { /* create vscale for storing dx */
ierr = VecCreateGhost(PetscObjectComm((PetscObject)mat),mat->cmap->n,PETSC_DETERMINE,B->cmap->n,aij->garray,&c->vscale);CHKERRQ(ierr);
}
}
m = mat->rmap->n/bs;
cstart = mat->cmap->rstart/bs;
cend = mat->cmap->rend/bs;
ierr = PetscMalloc1(nis,&c->ncolumns);CHKERRQ(ierr);
ierr = PetscMalloc1(nis,&c->columns);CHKERRQ(ierr);
ierr = PetscMalloc1(nis,&c->nrows);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)c,3*nis*sizeof(PetscInt));CHKERRQ(ierr);
if (c->htype[0] == 'd') {
ierr = PetscMalloc1(nz,&Jentry);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)c,nz*sizeof(MatEntry));CHKERRQ(ierr);
c->matentry = Jentry;
} else if (c->htype[0] == 'w') {
ierr = PetscMalloc1(nz,&Jentry2);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)c,nz*sizeof(MatEntry2));CHKERRQ(ierr);
c->matentry2 = Jentry2;
} else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"htype is not supported");
ierr = PetscMalloc2(m+1,&rowhit,m+1,&valaddrhit);CHKERRQ(ierr);
nz = 0;
ierr = ISColoringGetIS(iscoloring,PETSC_IGNORE,&isa);CHKERRQ(ierr);
for (i=0; i<nis; i++) { /* for each local color */
ierr = ISGetLocalSize(isa[i],&n);CHKERRQ(ierr);
ierr = ISGetIndices(isa[i],&is);CHKERRQ(ierr);
c->ncolumns[i] = n; /* local number of columns of this color on this process */
if (n) {
ierr = PetscMalloc1(n,&c->columns[i]);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)c,n*sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(c->columns[i],is,n*sizeof(PetscInt));CHKERRQ(ierr);
} else {
c->columns[i] = 0;
}
if (ctype == IS_COLORING_GLOBAL) {
/* Determine nctot, the total (parallel) number of columns of this color */
ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr);
ierr = PetscMalloc2(size,&ncolsonproc,size,&disp);CHKERRQ(ierr);
/* ncolsonproc[j]: local ncolumns on proc[j] of this color */
ierr = PetscMPIIntCast(n,&nn);CHKERRQ(ierr);
ierr = MPI_Allgather(&nn,1,MPI_INT,ncolsonproc,1,MPI_INT,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
nctot = 0; for (j=0; j<size; j++) nctot += ncolsonproc[j];
if (!nctot) {
ierr = PetscInfo(mat,"Coloring of matrix has some unneeded colors with no corresponding rows\n");CHKERRQ(ierr);
}
disp[0] = 0;
for (j=1; j<size; j++) {
disp[j] = disp[j-1] + ncolsonproc[j-1];
}
/* Get cols, the complete list of columns for this color on each process */
ierr = PetscMalloc1(nctot+1,&cols);CHKERRQ(ierr);
ierr = MPI_Allgatherv((void*)is,n,MPIU_INT,cols,ncolsonproc,disp,MPIU_INT,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr);
ierr = PetscFree2(ncolsonproc,disp);CHKERRQ(ierr);
} else if (ctype == IS_COLORING_GHOSTED) {
/* Determine local number of columns of this color on this process, including ghost points */
nctot = n;
ierr = PetscMalloc1(nctot+1,&cols);CHKERRQ(ierr);
ierr = PetscMemcpy(cols,is,n*sizeof(PetscInt));CHKERRQ(ierr);
} else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not provided for this MatFDColoring type");
/* Mark all rows affect by these columns */
ierr = PetscMemzero(rowhit,m*sizeof(PetscInt));CHKERRQ(ierr);
bs2 = bs*bs;
nrows_i = 0;
for (j=0; j<nctot; j++) { /* loop over columns*/
if (ctype == IS_COLORING_GHOSTED) {
col = ltog[cols[j]];
} else {
col = cols[j];
}
if (col >= cstart && col < cend) { /* column is in A, diagonal block of mat */
row = A_cj + A_ci[col-cstart];
nrows = A_ci[col-cstart+1] - A_ci[col-cstart];
nrows_i += nrows;
/* loop over columns of A marking them in rowhit */
for (k=0; k<nrows; k++) {
/* set valaddrhit for part A */
spidx = bs2*spidxA[A_ci[col-cstart] + k];
valaddrhit[*row] = &A_val[spidx];
rowhit[*row++] = col - cstart + 1; /* local column index */
}
} else { /* column is in B, off-diagonal block of mat */
#if defined(PETSC_USE_CTABLE)
ierr = PetscTableFind(colmap,col+1,&colb);CHKERRQ(ierr);
colb--;
#else
colb = colmap[col] - 1; /* local column index */
#endif
if (colb == -1) {
nrows = 0;
} else {
colb = colb/bs;
row = B_cj + B_ci[colb];
nrows = B_ci[colb+1] - B_ci[colb];
}
nrows_i += nrows;
/* loop over columns of B marking them in rowhit */
for (k=0; k<nrows; k++) {
/* set valaddrhit for part B */
spidx = bs2*spidxB[B_ci[colb] + k];
valaddrhit[*row] = &B_val[spidx];
rowhit[*row++] = colb + 1 + cend - cstart; /* local column index */
}
}
}
c->nrows[i] = nrows_i;
if (c->htype[0] == 'd') {
for (j=0; j<m; j++) {
if (rowhit[j]) {
Jentry[nz].row = j; /* local row index */
Jentry[nz].col = rowhit[j] - 1; /* local column index */
Jentry[nz].valaddr = valaddrhit[j]; /* address of mat value for this entry */
nz++;
}
}
} else { /* c->htype == 'wp' */
for (j=0; j<m; j++) {
if (rowhit[j]) {
Jentry2[nz].row = j; /* local row index */
Jentry2[nz].valaddr = valaddrhit[j]; /* address of mat value for this entry */
nz++;
}
}
}
ierr = PetscFree(cols);CHKERRQ(ierr);
}
if (bcols > 1) { /* reorder Jentry for faster MatFDColoringApply() */
ierr = MatFDColoringSetUpBlocked_AIJ_Private(mat,c,nz);CHKERRQ(ierr);
}
if (isBAIJ) {
ierr = MatRestoreColumnIJ_SeqBAIJ_Color(A,0,PETSC_FALSE,PETSC_FALSE,&ncols,&A_ci,&A_cj,&spidxA,NULL);CHKERRQ(ierr);
ierr = MatRestoreColumnIJ_SeqBAIJ_Color(B,0,PETSC_FALSE,PETSC_FALSE,&ncols,&B_ci,&B_cj,&spidxB,NULL);CHKERRQ(ierr);
ierr = PetscMalloc1(bs*mat->rmap->n,&c->dy);CHKERRQ(ierr);
} else {
ierr = MatRestoreColumnIJ_SeqAIJ_Color(A,0,PETSC_FALSE,PETSC_FALSE,&ncols,&A_ci,&A_cj,&spidxA,NULL);CHKERRQ(ierr);
ierr = MatRestoreColumnIJ_SeqAIJ_Color(B,0,PETSC_FALSE,PETSC_FALSE,&ncols,&B_ci,&B_cj,&spidxB,NULL);CHKERRQ(ierr);
}
ierr = ISColoringRestoreIS(iscoloring,&isa);CHKERRQ(ierr);
ierr = PetscFree2(rowhit,valaddrhit);CHKERRQ(ierr);
if (ctype == IS_COLORING_GHOSTED) {
ierr = ISLocalToGlobalMappingRestoreIndices(map,<og);CHKERRQ(ierr);
}
ierr = PetscInfo3(c,"ncolors %D, brows %D and bcols %D are used.\n",c->ncolors,c->brows,c->bcols);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
ISCompressIndicesGeneral - convert the indices into block indices
Input Parameters:
+ n - maximum possible length of the index set
. nkeys - expected number of keys when PETSC_USE_CTABLE
. bs - the size of block
. imax - the number of index sets
- is_in - the non-blocked array of index sets
Output Parameter:
. is_out - the blocked new index set
Level: intermediate
.seealso: ISExpandIndicesGeneral()
@*/
PetscErrorCode ISCompressIndicesGeneral(PetscInt n,PetscInt nkeys,PetscInt bs,PetscInt imax,const IS is_in[],IS is_out[])
{
PetscErrorCode ierr;
PetscInt isz,len,i,j,ival,Nbs;
const PetscInt *idx;
#if defined(PETSC_USE_CTABLE)
PetscTable gid1_lid1;
PetscInt tt, gid1, *nidx,Nkbs;
PetscTablePosition tpos;
#else
PetscInt *nidx;
PetscBT table;
#endif
PetscFunctionBegin;
Nbs =n/bs;
#if defined(PETSC_USE_CTABLE)
Nkbs = nkeys/bs;
ierr = PetscTableCreate(Nkbs,Nbs,&gid1_lid1);CHKERRQ(ierr);
#else
ierr = PetscMalloc1(Nbs,&nidx);CHKERRQ(ierr);
ierr = PetscBTCreate(Nbs,&table);CHKERRQ(ierr);
#endif
for (i=0; i<imax; i++) {
isz = 0;
#if defined(PETSC_USE_CTABLE)
ierr = PetscTableRemoveAll(gid1_lid1);CHKERRQ(ierr);
#else
ierr = PetscBTMemzero(Nbs,table);CHKERRQ(ierr);
#endif
ierr = ISGetIndices(is_in[i],&idx);CHKERRQ(ierr);
ierr = ISGetLocalSize(is_in[i],&len);CHKERRQ(ierr);
for (j=0; j<len; j++) {
ival = idx[j]/bs; /* convert the indices into block indices */
#if defined(PETSC_USE_CTABLE)
ierr = PetscTableFind(gid1_lid1,ival+1,&tt);CHKERRQ(ierr);
if (!tt) {
ierr = PetscTableAdd(gid1_lid1,ival+1,isz+1,INSERT_VALUES);CHKERRQ(ierr);
isz++;
}
#else
if (ival>Nbs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"index greater than mat-dim");
if (!PetscBTLookupSet(table,ival)) nidx[isz++] = ival;
#endif
}
ierr = ISRestoreIndices(is_in[i],&idx);CHKERRQ(ierr);
#if defined(PETSC_USE_CTABLE)
ierr = PetscMalloc1(isz,&nidx);CHKERRQ(ierr);
ierr = PetscTableGetHeadPosition(gid1_lid1,&tpos);CHKERRQ(ierr);
j = 0;
while (tpos) {
ierr = PetscTableGetNext(gid1_lid1,&tpos,&gid1,&tt);CHKERRQ(ierr);
if (tt-- > isz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"index greater than array-dim");
nidx[tt] = gid1 - 1;
j++;
}
if (j != isz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"table error: jj != isz");
ierr = ISCreateGeneral(PETSC_COMM_SELF,isz,nidx,PETSC_OWN_POINTER,(is_out+i));CHKERRQ(ierr);
#else
ierr = ISCreateGeneral(PETSC_COMM_SELF,isz,nidx,PETSC_COPY_VALUES,(is_out+i));CHKERRQ(ierr);
#endif
}
#if defined(PETSC_USE_CTABLE)
ierr = PetscTableDestroy(&gid1_lid1);CHKERRQ(ierr);
#else
ierr = PetscBTDestroy(&table);CHKERRQ(ierr);
ierr = PetscFree(nidx);CHKERRQ(ierr);
#endif
PetscFunctionReturn(0);
}
int Epetra_PETScAIJMatrix::ExtractMyRowCopy(int Row, int Length, int & NumEntries, double * Values,
int * Indices) const
{
int nz;
PetscInt *gcols, *lcols, ierr;
PetscScalar *vals;
bool alloc=false;
// PETSc assumes the row number is global, whereas Trilinos assumes it's local.
int globalRow = PetscRowStart_ + Row;
assert(globalRow < PetscRowEnd_);
ierr=MatGetRow(Amat_, globalRow, &nz, (const PetscInt**) &gcols, (const PetscScalar **) &vals);CHKERRQ(ierr);
// I ripped this bit of code from PETSc's MatSetValues_MPIAIJ() in mpiaij.c. The PETSc getrow returns everything in
// global numbering, so we must convert to local numbering.
if (strcmp(MatType_,MATMPIAIJ) == 0) {
Mat_MPIAIJ *aij = (Mat_MPIAIJ*)Amat_->data;
lcols = (PetscInt *) malloc(nz * sizeof(int));
alloc=true;
if (!aij->colmap) {
ierr = CreateColmap_MPIAIJ_Private(Amat_);CHKERRQ(ierr);
}
/*
A PETSc parallel aij matrix uses two matrices to represent the local rows.
The first matrix, A, is square and contains all local columns.
The second matrix, B, is rectangular and contains all non-local columns.
Matrix A:
Local column ID's are mapped to global column id's by adding cmap.rstart.
Given the global ID of a local column, the local ID is found by
subtracting cmap.rstart.
Matrix B:
Non-local column ID's are mapped to global column id's by the local-to-
global map garray. Given the global ID of a local column, the local ID is
found by the global-to-local map colmap. colmap is either an array or
hash table, the latter being the case when PETSC_USE_CTABLE is defined.
*/
int offset = Amat_->cmap->n-1; //offset for non-local column indices
for (int i=0; i<nz; i++) {
if (gcols[i] >= Amat_->cmap->rstart && gcols[i] < Amat_->cmap->rend) {
lcols[i] = gcols[i] - Amat_->cmap->rstart;
} else {
# ifdef PETSC_USE_CTABLE
ierr = PetscTableFind(aij->colmap,gcols[i]+1,lcols+i);CHKERRQ(ierr);
lcols[i] = lcols[i] + offset;
# else
lcols[i] = aij->colmap[gcols[i]] + offset;
# endif
}
} //for i=0; i<nz; i++)
}
else lcols = gcols;
NumEntries = nz;
if (NumEntries > Length) return(-1);
for (int i=0; i<NumEntries; i++) {
Indices[i] = lcols[i];
Values[i] = vals[i];
}
if (alloc) free(lcols);
MatRestoreRow(Amat_,globalRow,&nz,(const PetscInt**) &gcols, (const PetscScalar **) &vals);
return(0);
} //ExtractMyRowCopy()
/*
DMDAGetFaceInterpolation - Gets the interpolation for a face based coarse space
*/
PetscErrorCode DMDAGetFaceInterpolation(DM da,PC_Exotic *exotic,Mat Aglobal,MatReuse reuse,Mat *P)
{
PetscErrorCode ierr;
PetscInt dim,i,j,k,m,n,p,dof,Nint,Nface,Nwire,Nsurf,*Iint,*Isurf,cint = 0,csurf = 0,istart,jstart,kstart,*II,N,c = 0;
PetscInt mwidth,nwidth,pwidth,cnt,mp,np,pp,Ntotal,gl[6],*globals,Ng,*IIint,*IIsurf,Nt;
Mat Xint, Xsurf,Xint_tmp;
IS isint,issurf,is,row,col;
ISLocalToGlobalMapping ltg;
MPI_Comm comm;
Mat A,Aii,Ais,Asi,*Aholder,iAii;
MatFactorInfo info;
PetscScalar *xsurf,*xint;
#if defined(PETSC_USE_DEBUG_foo)
PetscScalar tmp;
#endif
PetscTable ht;
PetscFunctionBegin;
ierr = DMDAGetInfo(da,&dim,0,0,0,&mp,&np,&pp,&dof,0,0,0,0,0);
CHKERRQ(ierr);
if (dof != 1) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Only for single field problems");
if (dim != 3) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Only coded for 3d problems");
ierr = DMDAGetCorners(da,0,0,0,&m,&n,&p);
CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(da,&istart,&jstart,&kstart,&mwidth,&nwidth,&pwidth);
CHKERRQ(ierr);
istart = istart ? -1 : 0;
jstart = jstart ? -1 : 0;
kstart = kstart ? -1 : 0;
/*
the columns of P are the interpolation of each coarse grid point (one for each vertex and edge)
to all the local degrees of freedom (this includes the vertices, edges and faces).
Xint are the subset of the interpolation into the interior
Xface are the interpolation onto faces but not into the interior
Xsurf are the interpolation onto the vertices and edges (the surfbasket)
Xint
Symbolically one could write P = (Xface) after interchanging the rows to match the natural ordering on the domain
Xsurf
*/
N = (m - istart)*(n - jstart)*(p - kstart);
Nint = (m-2-istart)*(n-2-jstart)*(p-2-kstart);
Nface = 2*((m-2-istart)*(n-2-jstart) + (m-2-istart)*(p-2-kstart) + (n-2-jstart)*(p-2-kstart));
Nwire = 4*((m-2-istart) + (n-2-jstart) + (p-2-kstart)) + 8;
Nsurf = Nface + Nwire;
ierr = MatCreateSeqDense(MPI_COMM_SELF,Nint,6,NULL,&Xint);
CHKERRQ(ierr);
ierr = MatCreateSeqDense(MPI_COMM_SELF,Nsurf,6,NULL,&Xsurf);
CHKERRQ(ierr);
ierr = MatDenseGetArray(Xsurf,&xsurf);
CHKERRQ(ierr);
/*
Require that all 12 edges and 6 faces have at least one grid point. Otherwise some of the columns of
Xsurf will be all zero (thus making the coarse matrix singular).
*/
if (m-istart < 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Number of grid points per process in X direction must be at least 3");
if (n-jstart < 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Number of grid points per process in Y direction must be at least 3");
if (p-kstart < 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Number of grid points per process in Z direction must be at least 3");
cnt = 0;
for (j=1; j<n-1-jstart; j++) {
for (i=1; i<m-istart-1; i++) xsurf[cnt++ + 0*Nsurf] = 1;
}
for (k=1; k<p-1-kstart; k++) {
for (i=1; i<m-istart-1; i++) xsurf[cnt++ + 1*Nsurf] = 1;
for (j=1; j<n-1-jstart; j++) {
xsurf[cnt++ + 2*Nsurf] = 1;
/* these are the interior nodes */
xsurf[cnt++ + 3*Nsurf] = 1;
}
for (i=1; i<m-istart-1; i++) xsurf[cnt++ + 4*Nsurf] = 1;
}
for (j=1; j<n-1-jstart; j++) {
for (i=1; i<m-istart-1; i++) xsurf[cnt++ + 5*Nsurf] = 1;
}
#if defined(PETSC_USE_DEBUG_foo)
for (i=0; i<Nsurf; i++) {
tmp = 0.0;
for (j=0; j<6; j++) tmp += xsurf[i+j*Nsurf];
if (PetscAbsScalar(tmp-1.0) > 1.e-10) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Wrong Xsurf interpolation at i %D value %g",i,(double)PetscAbsScalar(tmp));
}
#endif
ierr = MatDenseRestoreArray(Xsurf,&xsurf);
CHKERRQ(ierr);
/* ierr = MatView(Xsurf,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);*/
/*
I are the indices for all the needed vertices (in global numbering)
Iint are the indices for the interior values, I surf for the surface values
(This is just for the part of the global matrix obtained with MatGetSubMatrix(), it
is NOT the local DMDA ordering.)
IIint and IIsurf are the same as the Iint, Isurf except they are in the global numbering
*/
#define Endpoint(a,start,b) (a == 0 || a == (b-1-start))
ierr = PetscMalloc3(N,&II,Nint,&Iint,Nsurf,&Isurf);
CHKERRQ(ierr);
ierr = PetscMalloc2(Nint,&IIint,Nsurf,&IIsurf);
CHKERRQ(ierr);
for (k=0; k<p-kstart; k++) {
for (j=0; j<n-jstart; j++) {
for (i=0; i<m-istart; i++) {
II[c++] = i + j*mwidth + k*mwidth*nwidth;
if (!Endpoint(i,istart,m) && !Endpoint(j,jstart,n) && !Endpoint(k,kstart,p)) {
IIint[cint] = i + j*mwidth + k*mwidth*nwidth;
Iint[cint++] = i + j*(m-istart) + k*(m-istart)*(n-jstart);
} else {
IIsurf[csurf] = i + j*mwidth + k*mwidth*nwidth;
Isurf[csurf++] = i + j*(m-istart) + k*(m-istart)*(n-jstart);
}
}
}
}
if (c != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"c != N");
if (cint != Nint) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"cint != Nint");
if (csurf != Nsurf) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"csurf != Nsurf");
ierr = DMGetLocalToGlobalMapping(da,<g);
CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApply(ltg,N,II,II);
CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApply(ltg,Nint,IIint,IIint);
CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApply(ltg,Nsurf,IIsurf,IIsurf);
CHKERRQ(ierr);
ierr = PetscObjectGetComm((PetscObject)da,&comm);
CHKERRQ(ierr);
ierr = ISCreateGeneral(comm,N,II,PETSC_COPY_VALUES,&is);
CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,Nint,Iint,PETSC_COPY_VALUES,&isint);
CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,Nsurf,Isurf,PETSC_COPY_VALUES,&issurf);
CHKERRQ(ierr);
ierr = PetscFree3(II,Iint,Isurf);
CHKERRQ(ierr);
ierr = ISSort(is);
CHKERRQ(ierr);
ierr = MatGetSubMatrices(Aglobal,1,&is,&is,MAT_INITIAL_MATRIX,&Aholder);
CHKERRQ(ierr);
A = *Aholder;
ierr = PetscFree(Aholder);
CHKERRQ(ierr);
ierr = MatGetSubMatrix(A,isint,isint,MAT_INITIAL_MATRIX,&Aii);
CHKERRQ(ierr);
ierr = MatGetSubMatrix(A,isint,issurf,MAT_INITIAL_MATRIX,&Ais);
CHKERRQ(ierr);
ierr = MatGetSubMatrix(A,issurf,isint,MAT_INITIAL_MATRIX,&Asi);
CHKERRQ(ierr);
/*
Solve for the interpolation onto the interior Xint
*/
ierr = MatMatMult(Ais,Xsurf,MAT_INITIAL_MATRIX,PETSC_DETERMINE,&Xint_tmp);
CHKERRQ(ierr);
ierr = MatScale(Xint_tmp,-1.0);
CHKERRQ(ierr);
if (exotic->directSolve) {
ierr = MatGetFactor(Aii,MATSOLVERPETSC,MAT_FACTOR_LU,&iAii);
CHKERRQ(ierr);
ierr = MatFactorInfoInitialize(&info);
CHKERRQ(ierr);
ierr = MatGetOrdering(Aii,MATORDERINGND,&row,&col);
CHKERRQ(ierr);
ierr = MatLUFactorSymbolic(iAii,Aii,row,col,&info);
CHKERRQ(ierr);
ierr = ISDestroy(&row);
CHKERRQ(ierr);
ierr = ISDestroy(&col);
CHKERRQ(ierr);
ierr = MatLUFactorNumeric(iAii,Aii,&info);
CHKERRQ(ierr);
ierr = MatMatSolve(iAii,Xint_tmp,Xint);
CHKERRQ(ierr);
ierr = MatDestroy(&iAii);
CHKERRQ(ierr);
} else {
Vec b,x;
PetscScalar *xint_tmp;
ierr = MatDenseGetArray(Xint,&xint);
CHKERRQ(ierr);
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,Nint,0,&x);
CHKERRQ(ierr);
ierr = MatDenseGetArray(Xint_tmp,&xint_tmp);
CHKERRQ(ierr);
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,Nint,0,&b);
CHKERRQ(ierr);
ierr = KSPSetOperators(exotic->ksp,Aii,Aii);
CHKERRQ(ierr);
for (i=0; i<6; i++) {
ierr = VecPlaceArray(x,xint+i*Nint);
CHKERRQ(ierr);
ierr = VecPlaceArray(b,xint_tmp+i*Nint);
CHKERRQ(ierr);
ierr = KSPSolve(exotic->ksp,b,x);
CHKERRQ(ierr);
ierr = VecResetArray(x);
CHKERRQ(ierr);
ierr = VecResetArray(b);
CHKERRQ(ierr);
}
ierr = MatDenseRestoreArray(Xint,&xint);
CHKERRQ(ierr);
ierr = MatDenseRestoreArray(Xint_tmp,&xint_tmp);
CHKERRQ(ierr);
ierr = VecDestroy(&x);
CHKERRQ(ierr);
ierr = VecDestroy(&b);
CHKERRQ(ierr);
}
ierr = MatDestroy(&Xint_tmp);
CHKERRQ(ierr);
#if defined(PETSC_USE_DEBUG_foo)
ierr = MatDenseGetArray(Xint,&xint);
CHKERRQ(ierr);
for (i=0; i<Nint; i++) {
tmp = 0.0;
for (j=0; j<6; j++) tmp += xint[i+j*Nint];
if (PetscAbsScalar(tmp-1.0) > 1.e-10) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Wrong Xint interpolation at i %D value %g",i,(double)PetscAbsScalar(tmp));
}
ierr = MatDenseRestoreArray(Xint,&xint);
CHKERRQ(ierr);
/* ierr =MatView(Xint,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */
#endif
/* total faces */
Ntotal = mp*np*(pp+1) + mp*pp*(np+1) + np*pp*(mp+1);
/*
For each vertex, edge, face on process (in the same orderings as used above) determine its local number including ghost points
*/
cnt = 0;
{
gl[cnt++] = mwidth+1;
}
{
{
gl[cnt++] = mwidth*nwidth+1;
}
{
gl[cnt++] = mwidth*nwidth + mwidth; /* these are the interior nodes */ gl[cnt++] = mwidth*nwidth + mwidth+m-istart-1;
}
{
gl[cnt++] = mwidth*nwidth+mwidth*(n-jstart-1)+1;
}
}
{
gl[cnt++] = mwidth*nwidth*(p-kstart-1) + mwidth+1;
}
/* PetscIntView(6,gl,PETSC_VIEWER_STDOUT_WORLD); */
/* convert that to global numbering and get them on all processes */
ierr = ISLocalToGlobalMappingApply(ltg,6,gl,gl);
CHKERRQ(ierr);
/* PetscIntView(6,gl,PETSC_VIEWER_STDOUT_WORLD); */
ierr = PetscMalloc1(6*mp*np*pp,&globals);
CHKERRQ(ierr);
ierr = MPI_Allgather(gl,6,MPIU_INT,globals,6,MPIU_INT,PetscObjectComm((PetscObject)da));
CHKERRQ(ierr);
/* Number the coarse grid points from 0 to Ntotal */
ierr = MatGetSize(Aglobal,&Nt,NULL);
CHKERRQ(ierr);
ierr = PetscTableCreate(Ntotal/3,Nt+1,&ht);
CHKERRQ(ierr);
for (i=0; i<6*mp*np*pp; i++) {
ierr = PetscTableAddCount(ht,globals[i]+1);
CHKERRQ(ierr);
}
ierr = PetscTableGetCount(ht,&cnt);
CHKERRQ(ierr);
if (cnt != Ntotal) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hash table size %D not equal to total number coarse grid points %D",cnt,Ntotal);
ierr = PetscFree(globals);
CHKERRQ(ierr);
for (i=0; i<6; i++) {
ierr = PetscTableFind(ht,gl[i]+1,&gl[i]);
CHKERRQ(ierr);
gl[i]--;
}
ierr = PetscTableDestroy(&ht);
CHKERRQ(ierr);
/* PetscIntView(6,gl,PETSC_VIEWER_STDOUT_WORLD); */
/* construct global interpolation matrix */
ierr = MatGetLocalSize(Aglobal,&Ng,NULL);
CHKERRQ(ierr);
if (reuse == MAT_INITIAL_MATRIX) {
ierr = MatCreateAIJ(PetscObjectComm((PetscObject)da),Ng,PETSC_DECIDE,PETSC_DECIDE,Ntotal,Nint+Nsurf,NULL,Nint,NULL,P);
CHKERRQ(ierr);
} else {
ierr = MatZeroEntries(*P);
CHKERRQ(ierr);
}
ierr = MatSetOption(*P,MAT_ROW_ORIENTED,PETSC_FALSE);
CHKERRQ(ierr);
ierr = MatDenseGetArray(Xint,&xint);
CHKERRQ(ierr);
ierr = MatSetValues(*P,Nint,IIint,6,gl,xint,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatDenseRestoreArray(Xint,&xint);
CHKERRQ(ierr);
ierr = MatDenseGetArray(Xsurf,&xsurf);
CHKERRQ(ierr);
ierr = MatSetValues(*P,Nsurf,IIsurf,6,gl,xsurf,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatDenseRestoreArray(Xsurf,&xsurf);
CHKERRQ(ierr);
ierr = MatAssemblyBegin(*P,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(*P,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = PetscFree2(IIint,IIsurf);
CHKERRQ(ierr);
#if defined(PETSC_USE_DEBUG_foo)
{
Vec x,y;
PetscScalar *yy;
ierr = VecCreateMPI(PetscObjectComm((PetscObject)da),Ng,PETSC_DETERMINE,&y);
CHKERRQ(ierr);
ierr = VecCreateMPI(PetscObjectComm((PetscObject)da),PETSC_DETERMINE,Ntotal,&x);
CHKERRQ(ierr);
ierr = VecSet(x,1.0);
CHKERRQ(ierr);
ierr = MatMult(*P,x,y);
CHKERRQ(ierr);
ierr = VecGetArray(y,&yy);
CHKERRQ(ierr);
for (i=0; i<Ng; i++) {
if (PetscAbsScalar(yy[i]-1.0) > 1.e-10) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Wrong p interpolation at i %D value %g",i,(double)PetscAbsScalar(yy[i]));
}
ierr = VecRestoreArray(y,&yy);
CHKERRQ(ierr);
ierr = VecDestroy(x);
CHKERRQ(ierr);
ierr = VecDestroy(y);
CHKERRQ(ierr);
}
#endif
ierr = MatDestroy(&Aii);
CHKERRQ(ierr);
ierr = MatDestroy(&Ais);
CHKERRQ(ierr);
ierr = MatDestroy(&Asi);
CHKERRQ(ierr);
ierr = MatDestroy(&A);
CHKERRQ(ierr);
ierr = ISDestroy(&is);
CHKERRQ(ierr);
ierr = ISDestroy(&isint);
CHKERRQ(ierr);
ierr = ISDestroy(&issurf);
CHKERRQ(ierr);
ierr = MatDestroy(&Xint);
CHKERRQ(ierr);
ierr = MatDestroy(&Xsurf);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatSetUpMultiply_MPIAIJ(Mat mat)
{
Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data;
Mat_SeqAIJ *B = (Mat_SeqAIJ*)(aij->B->data);
PetscErrorCode ierr;
PetscInt i,j,*aj = B->j,ec = 0,*garray;
IS from,to;
Vec gvec;
PetscBool useblockis;
#if defined (PETSC_USE_CTABLE)
PetscTable gid1_lid1;
PetscTablePosition tpos;
PetscInt gid,lid;
#else
PetscInt N = mat->cmap->N,*indices;
#endif
PetscFunctionBegin;
#if defined (PETSC_USE_CTABLE)
/* use a table */
ierr = PetscTableCreate(aij->B->rmap->n,mat->cmap->N+1,&gid1_lid1);CHKERRQ(ierr);
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
PetscInt data,gid1 = aj[B->i[i] + j] + 1;
ierr = PetscTableFind(gid1_lid1,gid1,&data);CHKERRQ(ierr);
if (!data) {
/* one based table */
ierr = PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
/* form array of columns we need */
ierr = PetscMalloc((ec+1)*sizeof(PetscInt),&garray);CHKERRQ(ierr);
ierr = PetscTableGetHeadPosition(gid1_lid1,&tpos);CHKERRQ(ierr);
while (tpos) {
ierr = PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);CHKERRQ(ierr);
gid--;
lid--;
garray[lid] = gid;
}
ierr = PetscSortInt(ec,garray);CHKERRQ(ierr); /* sort, and rebuild */
ierr = PetscTableRemoveAll(gid1_lid1);CHKERRQ(ierr);
for (i=0; i<ec; i++) {
ierr = PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr);
}
/* compact out the extra columns in B */
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
PetscInt gid1 = aj[B->i[i] + j] + 1;
ierr = PetscTableFind(gid1_lid1,gid1,&lid);CHKERRQ(ierr);
lid --;
aj[B->i[i] + j] = lid;
}
}
aij->B->cmap->n = aij->B->cmap->N = ec;
ierr = PetscLayoutSetUp((aij->B->cmap));CHKERRQ(ierr);
ierr = PetscTableDestroy(&gid1_lid1);CHKERRQ(ierr);
#else
/* Make an array as long as the number of columns */
/* mark those columns that are in aij->B */
ierr = PetscMalloc((N+1)*sizeof(PetscInt),&indices);CHKERRQ(ierr);
ierr = PetscMemzero(indices,N*sizeof(PetscInt));CHKERRQ(ierr);
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
if (!indices[aj[B->i[i] + j] ]) ec++;
indices[aj[B->i[i] + j] ] = 1;
}
}
/* form array of columns we need */
ierr = PetscMalloc((ec+1)*sizeof(PetscInt),&garray);CHKERRQ(ierr);
ec = 0;
for (i=0; i<N; i++) {
if (indices[i]) garray[ec++] = i;
}
/* make indices now point into garray */
for (i=0; i<ec; i++) {
indices[garray[i]] = i;
}
/* compact out the extra columns in B */
for (i=0; i<aij->B->rmap->n; i++) {
for (j=0; j<B->ilen[i]; j++) {
aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
}
}
aij->B->cmap->n = aij->B->cmap->N = ec;
ierr = PetscLayoutSetUp((aij->B->cmap));CHKERRQ(ierr);
ierr = PetscFree(indices);CHKERRQ(ierr);
#endif
/* create local vector that is used to scatter into */
ierr = VecCreateSeq(PETSC_COMM_SELF,ec,&aij->lvec);CHKERRQ(ierr);
/* create two temporary Index sets for build scatter gather */
/* check for the special case where blocks are communicated for faster VecScatterXXX */
useblockis = PETSC_FALSE;
if (mat->cmap->bs > 1) {
PetscInt bs = mat->cmap->bs,ibs,ga;
if (!(ec % bs)) {
useblockis = PETSC_TRUE;
for (i=0; i<ec/bs; i++) {
if ((ga = garray[ibs = i*bs]) % bs) {
useblockis = PETSC_FALSE;
break;
}
for (j=1; j<bs; j++) {
if (garray[ibs+j] != ga+j) {
useblockis = PETSC_FALSE;
break;
}
}
if (!useblockis) break;
}
}
}
#if defined(PETSC_USE_DEBUG)
i = (PetscInt)useblockis;
ierr = MPI_Allreduce(&i,&j,1,MPIU_INT,MPI_MIN,((PetscObject)mat)->comm); CHKERRQ(ierr);
if(j!=i) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Use of blocked not consistant (I am usning blocked)");
#endif
if (useblockis) {
PetscInt *ga,bs = mat->cmap->bs,iec = ec/bs;
if(ec%bs)SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"ec=%D bs=%D",ec,bs);
ierr = PetscInfo(mat,"Using block index set to define scatter\n");
ierr = PetscMalloc(iec*sizeof(PetscInt),&ga);CHKERRQ(ierr);
for (i=0; i<iec; i++) ga[i] = garray[i*bs]/bs;
ierr = ISCreateBlock(((PetscObject)mat)->comm,bs,iec,ga,PETSC_OWN_POINTER,&from);CHKERRQ(ierr);
} else {
ierr = ISCreateGeneral(((PetscObject)mat)->comm,ec,garray,PETSC_COPY_VALUES,&from);CHKERRQ(ierr);
}
ierr = ISCreateStride(PETSC_COMM_SELF,ec,0,1,&to);CHKERRQ(ierr);
/* create temporary global vector to generate scatter context */
/* This does not allocate the array's memory so is efficient */
ierr = VecCreateMPIWithArray(((PetscObject)mat)->comm,1,mat->cmap->n,mat->cmap->N,PETSC_NULL,&gvec);CHKERRQ(ierr);
/* generate the scatter context */
ierr = VecScatterCreate(gvec,from,aij->lvec,to,&aij->Mvctx);CHKERRQ(ierr);
ierr = PetscLogObjectParent(mat,aij->Mvctx);CHKERRQ(ierr);
ierr = PetscLogObjectParent(mat,aij->lvec);CHKERRQ(ierr);
ierr = PetscLogObjectParent(mat,from);CHKERRQ(ierr);
ierr = PetscLogObjectParent(mat,to);CHKERRQ(ierr);
aij->garray = garray;
ierr = PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));CHKERRQ(ierr);
ierr = ISDestroy(&from);CHKERRQ(ierr);
ierr = ISDestroy(&to);CHKERRQ(ierr);
ierr = VecDestroy(&gvec);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
