int CHOLMOD(colamd)
(
/* ---- input ---- */
cholmod_sparse *A, /* matrix to order */
Int *fset, /* subset of 0:(A->ncol)-1 */
size_t fsize, /* size of fset */
int postorder, /* if TRUE, follow with a coletree postorder */
/* ---- output --- */
Int *Perm, /* size A->nrow, output permutation */
/* --------------- */
cholmod_common *Common
)
{
double knobs [COLAMD_KNOBS] ;
cholmod_sparse *C ;
Int *NewPerm, *Parent, *Post, *Work2n ;
Int k, nrow, ncol ;
size_t s, alen ;
int ok = TRUE ;
/* ---------------------------------------------------------------------- */
/* check inputs */
/* ---------------------------------------------------------------------- */
RETURN_IF_NULL_COMMON (FALSE) ;
RETURN_IF_NULL (A, FALSE) ;
RETURN_IF_NULL (Perm, FALSE) ;
RETURN_IF_XTYPE_INVALID (A, CHOLMOD_PATTERN, CHOLMOD_ZOMPLEX, FALSE) ;
if (A->stype != 0)
{
ERROR (CHOLMOD_INVALID, "matrix must be unsymmetric") ;
return (FALSE) ;
}
Common->status = CHOLMOD_OK ;
/* ---------------------------------------------------------------------- */
/* get inputs */
/* ---------------------------------------------------------------------- */
nrow = A->nrow ;
ncol = A->ncol ;
/* ---------------------------------------------------------------------- */
/* allocate workspace */
/* ---------------------------------------------------------------------- */
/* Note: this is less than the space used in cholmod_analyze, so if
* cholmod_colamd is being called by that routine, no space will be
* allocated.
*/
/* s = 4*nrow + ncol */
s = CHOLMOD(mult_size_t) (nrow, 4, &ok) ;
s = CHOLMOD(add_size_t) (s, ncol, &ok) ;
#ifdef LONG
alen = colamd_l_recommended (A->nzmax, ncol, nrow) ;
colamd_l_set_defaults (knobs) ;
#else
alen = colamd_recommended (A->nzmax, ncol, nrow) ;
colamd_set_defaults (knobs) ;
#endif
if (!ok || alen == 0)
{
ERROR (CHOLMOD_TOO_LARGE, "matrix invalid or too large") ;
return (FALSE) ;
}
CHOLMOD(allocate_work) (0, s, 0, Common) ;
if (Common->status < CHOLMOD_OK)
{
return (FALSE) ;
}
/* ---------------------------------------------------------------------- */
/* allocate COLAMD workspace */
/* ---------------------------------------------------------------------- */
/* colamd_printf is only available in colamd v2.4 or later */
colamd_printf = Common->print_function ;
C = CHOLMOD(allocate_sparse) (ncol, nrow, alen, TRUE, TRUE, 0,
CHOLMOD_PATTERN, Common) ;
/* ---------------------------------------------------------------------- */
/* copy (and transpose) the input matrix A into the colamd workspace */
/* ---------------------------------------------------------------------- */
/* C = A (:,f)', which also packs A if needed. */
/* workspace: Iwork (nrow if no fset; MAX (nrow,ncol) if fset) */
ok = CHOLMOD(transpose_unsym) (A, 0, NULL, fset, fsize, C, Common) ;
/* ---------------------------------------------------------------------- */
/* order the matrix (destroys the contents of C->i and C->p) */
/* ---------------------------------------------------------------------- */
/* get parameters */
if (Common->current < 0 || Common->current >= CHOLMOD_MAXMETHODS)
{
/* this is the CHOLMOD default, not the COLAMD default */
knobs [COLAMD_DENSE_ROW] = -1 ;
}
else
{
/* get the knobs from the Common parameters */
knobs [COLAMD_DENSE_COL] = Common->method[Common->current].prune_dense ;
knobs [COLAMD_DENSE_ROW] = Common->method[Common->current].prune_dense2;
knobs [COLAMD_AGGRESSIVE] = Common->method[Common->current].aggressive ;
}
if (ok)
{
Int *Cp ;
Int stats [COLAMD_STATS] ;
Cp = C->p ;
#ifdef LONG
colamd_l (ncol, nrow, alen, C->i, Cp, knobs, stats) ;
#else
colamd (ncol, nrow, alen, C->i, Cp, knobs, stats) ;
#endif
ok = stats [COLAMD_STATUS] ;
ok = (ok == COLAMD_OK || ok == COLAMD_OK_BUT_JUMBLED) ;
/* permutation returned in C->p, if the ordering succeeded */
for (k = 0 ; k < nrow ; k++)
{
Perm [k] = Cp [k] ;
}
}
CHOLMOD(free_sparse) (&C, Common) ;
/* ---------------------------------------------------------------------- */
/* column etree postordering */
/* ---------------------------------------------------------------------- */
if (postorder)
{
/* use the last 2*n space in Iwork for Parent and Post */
Work2n = Common->Iwork ;
Work2n += 2*((size_t) nrow) + ncol ;
Parent = Work2n ; /* size nrow (i/i/l) */
Post = Work2n + nrow ; /* size nrow (i/i/l) */
/* workspace: Iwork (2*nrow+ncol), Flag (nrow), Head (nrow+1) */
ok = ok && CHOLMOD(analyze_ordering) (A, CHOLMOD_COLAMD, Perm, fset,
fsize, Parent, Post, NULL, NULL, NULL, Common) ;
/* combine the colamd permutation with its postordering */
if (ok)
{
NewPerm = Common->Iwork ; /* size nrow (i/i/l) */
for (k = 0 ; k < nrow ; k++)
{
NewPerm [k] = Perm [Post [k]] ;
}
for (k = 0 ; k < nrow ; k++)
{
Perm [k] = NewPerm [k] ;
}
}
}
return (ok) ;
}
void mexFunction
(
/* === Parameters ======================================================= */
int nlhs, /* number of left-hand sides */
mxArray *plhs [], /* left-hand side matrices */
int nrhs, /* number of right--hand sides */
const mxArray *prhs [] /* right-hand side matrices */
)
{
/* === Local variables ================================================== */
Long *perm ; /* column ordering of M and ordering of A */
Long *A ; /* row indices of input matrix A */
Long *p ; /* column pointers of input matrix A */
Long n_col ; /* number of columns of A */
Long n_row ; /* number of rows of A */
Long full ; /* TRUE if input matrix full, FALSE if sparse */
double knobs [COLAMD_KNOBS] ; /* colamd user-controllable parameters */
double *out_perm ; /* output permutation vector */
double *out_stats ; /* output stats vector */
double *in_knobs ; /* input knobs vector */
Long i ; /* loop counter */
mxArray *Ainput ; /* input matrix handle */
Long spumoni ; /* verbosity variable */
Long stats [COLAMD_STATS] ; /* stats for symamd */
colamd_printf = mexPrintf ; /* COLAMD printf routine */
/* === Check inputs ===================================================== */
if (nrhs < 1 || nrhs > 2 || nlhs < 0 || nlhs > 2)
{
mexErrMsgTxt (
"symamd: incorrect number of input and/or output arguments.") ;
}
/* === Get knobs ======================================================== */
colamd_l_set_defaults (knobs) ;
spumoni = 0 ;
/* check for user-passed knobs */
if (nrhs == 2)
{
in_knobs = mxGetPr (prhs [1]) ;
i = mxGetNumberOfElements (prhs [1]) ;
if (i > 0) knobs [COLAMD_DENSE_ROW] = in_knobs [0] ;
if (i > 1) spumoni = (Long) (in_knobs [1] != 0) ;
}
/* print knob settings if spumoni is set */
if (spumoni)
{
mexPrintf ("\nsymamd version %d.%d, %s:\n",
COLAMD_MAIN_VERSION, COLAMD_SUB_VERSION, COLAMD_DATE) ;
if (knobs [COLAMD_DENSE_ROW] >= 0)
{
mexPrintf ("knobs(1): %g, rows/cols with > "
"max(16,%g*sqrt(size(A,2))) entries removed\n",
in_knobs [0], knobs [COLAMD_DENSE_ROW]) ;
}
else
{
mexPrintf ("knobs(1): %g, no dense rows removed\n", in_knobs [0]) ;
}
mexPrintf ("knobs(2): %g, statistics and knobs printed\n",
in_knobs [1]) ;
}
/* === If A is full, convert to a sparse matrix ========================= */
Ainput = (mxArray *) prhs [0] ;
if (mxGetNumberOfDimensions (Ainput) != 2)
{
mexErrMsgTxt ("symamd: input matrix must be 2-dimensional.") ;
}
full = !mxIsSparse (Ainput) ;
if (full)
{
mexCallMATLAB (1, &Ainput, 1, (mxArray **) prhs, "sparse") ;
}
/* === Allocate workspace for symamd ==================================== */
/* get size of matrix */
n_row = mxGetM (Ainput) ;
n_col = mxGetN (Ainput) ;
if (n_col != n_row)
{
mexErrMsgTxt ("symamd: matrix must be square.") ;
}
A = (Long *) mxGetIr (Ainput) ;
p = (Long *) mxGetJc (Ainput) ;
perm = (Long *) mxCalloc (n_col+1, sizeof (Long)) ;
/* === Order the rows and columns of A (does not destroy A) ============= */
if (!symamd_l (n_col, A, p, perm, knobs, stats, &mxCalloc, &mxFree))
{
symamd_l_report (stats) ;
mexErrMsgTxt ("symamd error!") ;
}
if (full)
{
mxDestroyArray (Ainput) ;
}
/* === Return the permutation vector ==================================== */
plhs [0] = mxCreateDoubleMatrix (1, n_col, mxREAL) ;
out_perm = mxGetPr (plhs [0]) ;
for (i = 0 ; i < n_col ; i++)
{
/* symamd is 0-based, but MATLAB expects this to be 1-based */
out_perm [i] = perm [i] + 1 ;
}
mxFree (perm) ;
/* === Return the stats vector ========================================== */
/* print stats if spumoni is set */
if (spumoni)
{
symamd_l_report (stats) ;
}
if (nlhs == 2)
{
plhs [1] = mxCreateDoubleMatrix (1, COLAMD_STATS, mxREAL) ;
out_stats = mxGetPr (plhs [1]) ;
for (i = 0 ; i < COLAMD_STATS ; i++)
{
out_stats [i] = stats [i] ;
}
/* fix stats (5) and (6), for 1-based information on jumbled matrix. */
/* note that this correction doesn't occur if symamd returns FALSE */
out_stats [COLAMD_INFO1] ++ ;
out_stats [COLAMD_INFO2] ++ ;
}
}
void mexFunction
(
/* === Parameters ======================================================= */
int nlhs, /* number of left-hand sides */
mxArray *plhs [], /* left-hand side matrices */
int nrhs, /* number of right--hand sides */
const mxArray *prhs [] /* right-hand side matrices */
)
{
/* === Local variables ================================================== */
Long *perm ; /* column ordering of M and ordering of A */
Long *A ; /* row indices of input matrix A */
Long *p ; /* column pointers of input matrix A */
Long n_col ; /* number of columns of A */
Long n_row ; /* number of rows of A */
Long full ; /* TRUE if input matrix full, FALSE if sparse */
double knobs [COLAMD_KNOBS] ; /* colamd user-controllable parameters */
double *out_perm ; /* output permutation vector */
double *out_stats ; /* output stats vector */
double *in_knobs ; /* input knobs vector */
Long i ; /* loop counter */
mxArray *Ainput ; /* input matrix handle */
Long spumoni ; /* verbosity variable */
Long stats2 [COLAMD_STATS] ;/* stats for symamd */
Long *cp, *cp_end, result, nnz, col, length ;
Long *stats ;
stats = stats2 ;
/* === Check inputs ===================================================== */
if (nrhs < 1 || nrhs > 2 || nlhs < 0 || nlhs > 2)
{
mexErrMsgTxt (
"symamd: incorrect number of input and/or output arguments.") ;
}
if (nrhs != 2)
{
mexErrMsgTxt ("symamdtest: knobs are required") ;
}
/* for testing we require all 3 knobs */
if (mxGetNumberOfElements (prhs [1]) != 3)
{
mexErrMsgTxt ("symamdtest: must have all 3 knobs for testing") ;
}
/* === Get knobs ======================================================== */
colamd_l_set_defaults (knobs) ;
spumoni = 0 ;
/* check for user-passed knobs */
if (nrhs == 2)
{
in_knobs = mxGetPr (prhs [1]) ;
i = mxGetNumberOfElements (prhs [1]) ;
if (i > 0) knobs [COLAMD_DENSE_ROW] = in_knobs [0] ;
if (i > 1) spumoni = (Long) in_knobs [1] ;
}
/* print knob settings if spumoni is set */
if (spumoni)
{
mexPrintf ("\nsymamd version %d.%d, %s:\n",
COLAMD_MAIN_VERSION, COLAMD_SUB_VERSION, COLAMD_DATE) ;
if (knobs [COLAMD_DENSE_ROW] >= 0)
{
mexPrintf ("knobs(1): %g, rows/cols with > "
"max(16,%g*sqrt(size(A,2))) entries removed\n",
in_knobs [0], knobs [COLAMD_DENSE_ROW]) ;
}
else
{
mexPrintf ("knobs(1): %g, no dense rows removed\n", in_knobs [0]) ;
}
mexPrintf ("knobs(2): %g, statistics and knobs printed\n",
in_knobs [1]) ;
mexPrintf ("Testing %d\n", in_knobs [2]) ;
}
/* === If A is full, convert to a sparse matrix ========================= */
Ainput = (mxArray *) prhs [0] ;
if (mxGetNumberOfDimensions (Ainput) != 2)
{
mexErrMsgTxt ("symamd: input matrix must be 2-dimensional.") ;
}
full = !mxIsSparse (Ainput) ;
if (full)
{
mexCallMATLAB (1, &Ainput, 1, (mxArray **) prhs, "sparse") ;
}
/* === Allocate workspace for symamd ==================================== */
/* get size of matrix */
n_row = mxGetM (Ainput) ;
n_col = mxGetN (Ainput) ;
if (n_col != n_row)
{
mexErrMsgTxt ("symamd: matrix must be square.") ;
}
/* p = mxGetJc (Ainput) ; */
p = (Long *) mxCalloc (n_col+1, sizeof (Long)) ;
(void) memcpy (p, mxGetJc (Ainput), (n_col+1)*sizeof (Long)) ;
nnz = p [n_col] ;
if (spumoni > 0)
{
mexPrintf ("symamdtest: nnz %d\n", nnz) ;
}
/* A = mxGetIr (Ainput) ; */
A = (Long *) mxCalloc (nnz+1, sizeof (Long)) ;
(void) memcpy (A, mxGetIr (Ainput), nnz*sizeof (Long)) ;
perm = (Long *) mxCalloc (n_col+1, sizeof (Long)) ;
/* === Jumble matrix ======================================================== */
/*
knobs [2] FOR TESTING ONLY: Specifies how to jumble matrix
0 : No jumbling
1 : (no errors)
2 : Make first pointer non-zero
3 : Make column pointers not non-decreasing
4 : (no errors)
5 : Make row indices not strictly increasing
6 : Make a row index greater or equal to n_row
7 : Set A = NULL
8 : Set p = NULL
9 : Repeat row index
10: make row indices not sorted
11: jumble columns massively (note this changes
the pattern of the matrix A.)
12: Set stats = NULL
13: Make n_col less than zero
*/
/* jumble appropriately */
switch ((Long) in_knobs [2])
{
case 0 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: no errors expected\n") ;
}
result = 1 ; /* no errors */
break ;
case 1 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: no errors expected (1)\n") ;
}
result = 1 ;
break ;
case 2 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: p [0] nonzero\n") ;
}
result = 0 ; /* p [0] must be zero */
p [0] = 1 ;
break ;
case 3 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: negative length last column\n") ;
}
result = (n_col == 0) ; /* p must be monotonically inc. */
p [n_col] = p [0] ;
break ;
case 4 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: no errors expected (4)\n") ;
}
result = 1 ;
break ;
case 5 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: row index out of range (-1)\n") ;
}
if (nnz > 0) /* row index out of range */
{
result = 0 ;
A [nnz-1] = -1 ;
}
else
{
if (spumoni > 0)
{
mexPrintf ("Note: no row indices to put out of range\n") ;
}
result = 1 ;
}
break ;
case 6 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: row index out of range (ncol)\n") ;
}
if (nnz > 0) /* row index out of range */
{
result = 0 ;
A [nnz-1] = n_col ;
}
else
{
if (spumoni > 0)
{
mexPrintf ("Note: no row indices to put out of range\n") ;
}
result = 1 ;
}
break ;
case 7 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: A not present\n") ;
}
result = 0 ; /* A not present */
A = (Long *) NULL ;
break ;
case 8 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: p not present\n") ;
}
result = 0 ; /* p not present */
p = (Long *) NULL ;
break ;
case 9 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: duplicate row index\n") ;
}
result = 1 ; /* duplicate row index */
for (col = 0 ; col < n_col ; col++)
{
length = p [col+1] - p [col] ;
if (length > 1)
{
A [p [col+1]-2] = A [p [col+1] - 1] ;
if (spumoni > 0)
{
mexPrintf ("Made duplicate row %d in col %d\n",
A [p [col+1] - 1], col) ;
}
break ;
}
}
if (spumoni > 1)
{
dump_matrix (A, p, n_row, n_col, nnz, col+2) ;
}
break ;
case 10 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: unsorted column\n") ;
}
result = 1 ; /* jumbled columns */
for (col = 0 ; col < n_col ; col++)
{
length = p [col+1] - p [col] ;
if (length > 1)
{
i = A[p [col]] ;
A [p [col]] = A[p [col] + 1] ;
A [p [col] + 1] = i ;
if (spumoni > 0)
{
mexPrintf ("Unsorted column %d \n", col) ;
}
break ;
}
}
if (spumoni > 1)
{
dump_matrix (A, p, n_row, n_col, nnz, col+2) ;
}
break ;
case 11 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: massive jumbling\n") ;
}
result = 1 ; /* massive jumbling, but no errors */
srand (1) ;
for (i = 0 ; i < n_col ; i++)
{
cp = &A [p [i]] ;
cp_end = &A [p [i+1]] ;
while (cp < cp_end)
{
*cp++ = rand() % n_row ;
}
}
if (spumoni > 1)
{
dump_matrix (A, p, n_row, n_col, nnz, n_col) ;
}
break ;
case 12 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: stats not present\n") ;
}
result = 0 ; /* stats not present */
stats = (Long *) NULL ;
break ;
case 13 :
if (spumoni > 0)
{
mexPrintf ("symamdtest: ncol out of range\n") ;
}
result = 0 ; /* ncol out of range */
n_col = -1 ;
break ;
}
/* === Order the rows and columns of A (does not destroy A) ============= */
if (!symamd_l (n_col, A, p, perm, knobs, stats, &mxCalloc, &mxFree))
{
/* return p = -1 if colamd failed */
plhs [0] = mxCreateDoubleMatrix (1, 1, mxREAL) ;
out_perm = mxGetPr (plhs [0]) ;
out_perm [0] = -1 ;
mxFree (p) ;
mxFree (A) ;
if (spumoni > 0 || result)
{
symamd_l_report (stats) ;
}
if (result)
{
mexErrMsgTxt ("symamd should have returned TRUE\n") ;
}
return ;
/* mexErrMsgTxt ("symamd error!") ; */
}
if (!result)
{
symamd_l_report (stats) ;
mexErrMsgTxt ("symamd should have returned FALSE\n") ;
}
if (full)
{
mxDestroyArray (Ainput) ;
}
/* === Return the permutation vector ==================================== */
plhs [0] = mxCreateDoubleMatrix (1, n_col, mxREAL) ;
out_perm = mxGetPr (plhs [0]) ;
for (i = 0 ; i < n_col ; i++)
{
/* symamd is 0-based, but MATLAB expects this to be 1-based */
out_perm [i] = perm [i] + 1 ;
}
mxFree (perm) ;
/* === Return the stats vector ========================================== */
/* print stats if spumoni > 0 */
if (spumoni > 0)
{
symamd_l_report (stats) ;
}
if (nlhs == 2)
{
plhs [1] = mxCreateDoubleMatrix (1, COLAMD_STATS, mxREAL) ;
out_stats = mxGetPr (plhs [1]) ;
for (i = 0 ; i < COLAMD_STATS ; i++)
{
out_stats [i] = stats [i] ;
}
/* fix stats (5) and (6), for 1-based information on jumbled matrix. */
/* note that this correction doesn't occur if symamd returns FALSE */
out_stats [COLAMD_INFO1] ++ ;
out_stats [COLAMD_INFO2] ++ ;
}
}
