PetscErrorCode DMCreateColoring_Composite(DM dm,ISColoringType ctype,MatType mtype,ISColoring *coloring)
{
PetscErrorCode ierr;
PetscInt n,i,cnt;
ISColoringValue *colors;
PetscBool dense = PETSC_FALSE;
ISColoringValue maxcol = 0;
DM_Composite *com = (DM_Composite*)dm->data;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
if (ctype == IS_COLORING_GHOSTED) SETERRQ(((PetscObject)dm)->comm,PETSC_ERR_SUP,"Only global coloring supported" );
else if (ctype == IS_COLORING_GLOBAL) {
n = com->n;
} else SETERRQ(((PetscObject)dm)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Unknown ISColoringType");
ierr = PetscMalloc(n*sizeof(ISColoringValue),&colors);CHKERRQ(ierr); /* freed in ISColoringDestroy() */
ierr = PetscOptionsGetBool(PETSC_NULL,"-dmcomposite_dense_jacobian",&dense,PETSC_NULL);CHKERRQ(ierr);
if (dense) {
for (i=0; i<n; i++) {
colors[i] = (ISColoringValue)(com->rstart + i);
}
maxcol = com->N;
} else {
struct DMCompositeLink *next = com->next;
PetscMPIInt rank;
ierr = MPI_Comm_rank(((PetscObject)dm)->comm,&rank);CHKERRQ(ierr);
cnt = 0;
while (next) {
ISColoring lcoloring;
ierr = DMCreateColoring(next->dm,IS_COLORING_GLOBAL,mtype,&lcoloring);CHKERRQ(ierr);
for (i=0; i<lcoloring->N; i++) {
colors[cnt++] = maxcol + lcoloring->colors[i];
}
maxcol += lcoloring->n;
ierr = ISColoringDestroy(&lcoloring);CHKERRQ(ierr);
next = next->next;
}
}
ierr = ISColoringCreate(((PetscObject)dm)->comm,maxcol,n,colors,coloring);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode MatColoringApply_Greedy(MatColoring mc,ISColoring *iscoloring)
{
PetscErrorCode ierr;
PetscInt finalcolor,finalcolor_global;
ISColoringValue *colors;
PetscInt ncolstotal,ncols;
PetscReal *wts;
PetscInt i,*lperm;
PetscFunctionBegin;
ierr = MatGetSize(mc->mat,NULL,&ncolstotal);CHKERRQ(ierr);
ierr = MatGetLocalSize(mc->mat,NULL,&ncols);CHKERRQ(ierr);
if (!mc->user_weights) {
ierr = MatColoringCreateWeights(mc,&wts,&lperm);CHKERRQ(ierr);
} else {
wts = mc->user_weights;
lperm = mc->user_lperm;
}
ierr = PetscMalloc1(ncols,&colors);CHKERRQ(ierr);
if (mc->dist == 1) {
ierr = GreedyColoringLocalDistanceOne_Private(mc,wts,lperm,colors);CHKERRQ(ierr);
} else if (mc->dist == 2) {
ierr = GreedyColoringLocalDistanceTwo_Private(mc,wts,lperm,colors);CHKERRQ(ierr);
} else SETERRQ(PetscObjectComm((PetscObject)mc),PETSC_ERR_ARG_OUTOFRANGE,"Only distance 1 and distance 2 supported by MatColoringGreedy");
finalcolor=0;
for (i=0;i<ncols;i++) {
if (colors[i] > finalcolor) finalcolor=colors[i];
}
finalcolor_global=0;
ierr = MPIU_Allreduce(&finalcolor,&finalcolor_global,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)mc));CHKERRQ(ierr);
ierr = PetscLogEventBegin(MATCOLORING_ISCreate,mc,0,0,0);CHKERRQ(ierr);
ierr = ISColoringCreate(PetscObjectComm((PetscObject)mc),finalcolor_global+1,ncols,colors,PETSC_OWN_POINTER,iscoloring);CHKERRQ(ierr);
ierr = PetscLogEventEnd(MATCOLORING_ISCreate,mc,0,0,0);CHKERRQ(ierr);
if (!mc->user_weights) {
ierr = PetscFree(wts);CHKERRQ(ierr);
ierr = PetscFree(lperm);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode DMCreateColoring_Redundant(DM dm,ISColoringType ctype,ISColoring *coloring)
{
DM_Redundant *red = (DM_Redundant*)dm->data;
PetscErrorCode ierr;
PetscInt i,nloc;
ISColoringValue *colors;
PetscFunctionBegin;
switch (ctype) {
case IS_COLORING_GLOBAL:
nloc = red->n;
break;
case IS_COLORING_GHOSTED:
nloc = red->N;
break;
default: SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_WRONG,"Unknown ISColoringType %d",(int)ctype);
}
ierr = PetscMalloc1(nloc,&colors);CHKERRQ(ierr);
for (i=0; i<nloc; i++) colors[i] = i;
ierr = ISColoringCreate(PetscObjectComm((PetscObject)dm),red->N,nloc,colors,coloring);CHKERRQ(ierr);
ierr = ISColoringSetType(*coloring,ctype);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
EXTERN_C_BEGIN
/* ----------------------------------------------------------------------------*/
/*
MatGetColoring_SL_Minpack - Uses the smallest-last (SL) coloring of minpack
*/
#undef __FUNCT__
#define __FUNCT__ "MatGetColoring_SL_Minpack"
PetscErrorCode MatGetColoring_SL_Minpack(Mat mat,MatColoringType name,ISColoring *iscoloring)
{
PetscErrorCode ierr;
PetscInt *list,*work,clique,*seq,*coloring,n;
const PetscInt *ria,*rja,*cia,*cja;
PetscInt ncolors,i;
PetscBool done;
Mat mat_seq = mat;
PetscMPIInt size;
MPI_Comm comm;
ISColoring iscoloring_seq;
PetscInt bs = 1,rstart,rend,N_loc,nc;
ISColoringValue *colors_loc;
PetscBool flg1,flg2;
PetscFunctionBegin;
/* this is ugly way to get blocksize but cannot call MatGetBlockSize() because AIJ can have bs > 1 */
ierr = PetscObjectTypeCompare((PetscObject)mat,MATSEQBAIJ,&flg1);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)mat,MATMPIBAIJ,&flg2);CHKERRQ(ierr);
if (flg1 || flg2) {
ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr);
}
ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
if (size > 1){
/* create a sequential iscoloring on all processors */
ierr = MatGetSeqNonzeroStructure(mat,&mat_seq);CHKERRQ(ierr);
}
ierr = MatGetRowIJ(mat_seq,1,PETSC_FALSE,PETSC_TRUE,&n,&ria,&rja,&done);CHKERRQ(ierr);
ierr = MatGetColumnIJ(mat_seq,1,PETSC_FALSE,PETSC_TRUE,&n,&cia,&cja,&done);CHKERRQ(ierr);
if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Ordering requires IJ");
ierr = MatFDColoringDegreeSequence_Minpack(n,cja,cia,rja,ria,&seq);CHKERRQ(ierr);
ierr = PetscMalloc2(n,PetscInt,&list,4*n,PetscInt,&work);CHKERRQ(ierr);
MINPACKslo(&n,cja,cia,rja,ria,seq,list,&clique,work,work+n,work+2*n,work+3*n);
ierr = PetscMalloc(n*sizeof(PetscInt),&coloring);CHKERRQ(ierr);
MINPACKseq(&n,cja,cia,rja,ria,list,coloring,&ncolors,work);
ierr = PetscFree2(list,work);CHKERRQ(ierr);
ierr = PetscFree(seq);CHKERRQ(ierr);
ierr = MatRestoreRowIJ(mat_seq,1,PETSC_FALSE,PETSC_TRUE,&n,&ria,&rja,&done);CHKERRQ(ierr);
ierr = MatRestoreColumnIJ(mat_seq,1,PETSC_FALSE,PETSC_TRUE,&n,&cia,&cja,&done);CHKERRQ(ierr);
/* shift coloring numbers to start at zero and shorten */
if (ncolors > IS_COLORING_MAX-1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Maximum color size exceeded");
{
ISColoringValue *s = (ISColoringValue*) coloring;
for (i=0; i<n; i++) {
s[i] = (ISColoringValue) (coloring[i]-1);
}
ierr = MatColoringPatch(mat_seq,ncolors,n,s,iscoloring);CHKERRQ(ierr);
}
if (size > 1) {
ierr = MatDestroySeqNonzeroStructure(&mat_seq);CHKERRQ(ierr);
/* convert iscoloring_seq to a parallel iscoloring */
iscoloring_seq = *iscoloring;
rstart = mat->rmap->rstart/bs;
rend = mat->rmap->rend/bs;
N_loc = rend - rstart; /* number of local nodes */
/* get local colors for each local node */
ierr = PetscMalloc((N_loc+1)*sizeof(ISColoringValue),&colors_loc);CHKERRQ(ierr);
for (i=rstart; i<rend; i++){
colors_loc[i-rstart] = iscoloring_seq->colors[i];
}
/* create a parallel iscoloring */
nc=iscoloring_seq->n;
ierr = ISColoringCreate(comm,nc,N_loc,colors_loc,iscoloring);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring_seq);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
EXTERN_C_END
EXTERN_C_BEGIN
/*
Simplest coloring, each column of the matrix gets its own unique color.
*/
#undef __FUNCT__
#define __FUNCT__ "MatGetColoring_Natural"
PetscErrorCode MatGetColoring_Natural(Mat mat,MatColoringType color, ISColoring *iscoloring)
{
PetscErrorCode ierr;
PetscInt start,end,i,bs = 1,n;
ISColoringValue *colors;
MPI_Comm comm;
PetscBool flg1,flg2;
Mat mat_seq = mat;
PetscMPIInt size;
ISColoring iscoloring_seq;
ISColoringValue *colors_loc;
PetscInt rstart,rend,N_loc,nc;
PetscFunctionBegin;
/* this is ugly way to get blocksize but cannot call MatGetBlockSize() because AIJ can have bs > 1 */
ierr = PetscObjectTypeCompare((PetscObject)mat,MATSEQBAIJ,&flg1);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)mat,MATMPIBAIJ,&flg2);CHKERRQ(ierr);
if (flg1 || flg2) {
ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr);
}
ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
if (size > 1){
/* create a sequential iscoloring on all processors */
ierr = MatGetSeqNonzeroStructure(mat,&mat_seq);CHKERRQ(ierr);
}
ierr = MatGetSize(mat_seq,PETSC_NULL,&n);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(mat_seq,&start,&end);CHKERRQ(ierr);
n = n/bs;
if (n > IS_COLORING_MAX-1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Maximum color size exceeded");
start = start/bs;
end = end/bs;
ierr = PetscMalloc((end-start+1)*sizeof(PetscInt),&colors);CHKERRQ(ierr);
for (i=start; i<end; i++) {
colors[i-start] = (ISColoringValue)i;
}
ierr = ISColoringCreate(comm,n,end-start,colors,iscoloring);CHKERRQ(ierr);
if (size > 1) {
ierr = MatDestroySeqNonzeroStructure(&mat_seq);CHKERRQ(ierr);
/* convert iscoloring_seq to a parallel iscoloring */
iscoloring_seq = *iscoloring;
rstart = mat->rmap->rstart/bs;
rend = mat->rmap->rend/bs;
N_loc = rend - rstart; /* number of local nodes */
/* get local colors for each local node */
ierr = PetscMalloc((N_loc+1)*sizeof(ISColoringValue),&colors_loc);CHKERRQ(ierr);
for (i=rstart; i<rend; i++){
colors_loc[i-rstart] = iscoloring_seq->colors[i];
}
/* create a parallel iscoloring */
nc=iscoloring_seq->n;
ierr = ISColoringCreate(comm,nc,N_loc,colors_loc,iscoloring);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring_seq);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode MatColoringApply_LF(MatColoring mc,ISColoring *iscoloring)
{
PetscErrorCode ierr;
PetscInt *list,*work,*seq,*coloring,n;
const PetscInt *ria,*rja,*cia,*cja;
PetscInt n1, none,ncolors,i;
PetscBool done;
Mat mat = mc->mat;
Mat mat_seq = mat;
PetscMPIInt size;
MPI_Comm comm;
ISColoring iscoloring_seq;
PetscInt bs = 1,rstart,rend,N_loc,nc;
ISColoringValue *colors_loc;
PetscBool flg1,flg2;
PetscFunctionBegin;
if (mc->dist != 2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"LF may only do distance 2 coloring");
/* this is ugly way to get blocksize but cannot call MatGetBlockSize() because AIJ can have bs > 1 */
ierr = PetscObjectTypeCompare((PetscObject)mat,MATSEQBAIJ,&flg1);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)mat,MATMPIBAIJ,&flg2);CHKERRQ(ierr);
if (flg1 || flg2) {
ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr);
}
ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
if (size > 1) {
/* create a sequential iscoloring on all processors */
ierr = MatGetSeqNonzeroStructure(mat,&mat_seq);CHKERRQ(ierr);
}
ierr = MatGetRowIJ(mat_seq,1,PETSC_FALSE,PETSC_TRUE,&n,&ria,&rja,&done);CHKERRQ(ierr);
ierr = MatGetColumnIJ(mat_seq,1,PETSC_FALSE,PETSC_TRUE,&n,&cia,&cja,&done);CHKERRQ(ierr);
if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Ordering requires IJ");
ierr = MatFDColoringDegreeSequence_Minpack(n,cja,cia,rja,ria,&seq);CHKERRQ(ierr);
ierr = PetscMalloc2(n,&list,4*n,&work);CHKERRQ(ierr);
n1 = n - 1;
none = -1;
MINPACKnumsrt(&n,&n1,seq,&none,list,work+2*n,work+n);
ierr = PetscMalloc1(n,&coloring);CHKERRQ(ierr);
MINPACKseq(&n,cja,cia,rja,ria,list,coloring,&ncolors,work);
ierr = PetscFree2(list,work);CHKERRQ(ierr);
ierr = PetscFree(seq);CHKERRQ(ierr);
ierr = MatRestoreRowIJ(mat_seq,1,PETSC_FALSE,PETSC_TRUE,NULL,&ria,&rja,&done);CHKERRQ(ierr);
ierr = MatRestoreColumnIJ(mat_seq,1,PETSC_FALSE,PETSC_TRUE,NULL,&cia,&cja,&done);CHKERRQ(ierr);
/* shift coloring numbers to start at zero and shorten */
if (ncolors > IS_COLORING_MAX-1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Maximum color size exceeded");
{
ISColoringValue *s = (ISColoringValue*) coloring;
for (i=0; i<n; i++) s[i] = (ISColoringValue) (coloring[i]-1);
ierr = MatColoringPatch(mat_seq,ncolors,n,s,iscoloring);CHKERRQ(ierr);
}
if (size > 1) {
ierr = MatDestroySeqNonzeroStructure(&mat_seq);CHKERRQ(ierr);
/* convert iscoloring_seq to a parallel iscoloring */
iscoloring_seq = *iscoloring;
rstart = mat->rmap->rstart/bs;
rend = mat->rmap->rend/bs;
N_loc = rend - rstart; /* number of local nodes */
/* get local colors for each local node */
ierr = PetscMalloc1((N_loc+1),&colors_loc);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) colors_loc[i-rstart] = iscoloring_seq->colors[i];
/* create a parallel iscoloring */
nc = iscoloring_seq->n;
ierr = ISColoringCreate(comm,nc,N_loc,colors_loc,iscoloring);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring_seq);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
