int CHOLMOD(csymamd)
(
/* ---- input ---- */
cholmod_sparse *A, /* matrix to order */
/* ---- output --- */
Int *Cmember, /* size nrow. see cholmod_ccolamd.c for description */
Int *Perm, /* size A->nrow, output permutation */
/* --------------- */
cholmod_common *Common
)
{
double knobs [CCOLAMD_KNOBS] ;
Int *perm, *Head ;
Int ok, i, nrow, stats [CCOLAMD_STATS] ;
/* ---------------------------------------------------------------------- */
/* 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) ;
Common->status = CHOLMOD_OK ;
if (A->nrow != A->ncol || !(A->packed))
{
ERROR (CHOLMOD_INVALID, "matrix must be square and packed") ;
return (FALSE) ;
}
/* ---------------------------------------------------------------------- */
/* get inputs */
/* ---------------------------------------------------------------------- */
nrow = A->nrow ;
/* ---------------------------------------------------------------------- */
/* allocate workspace */
/* ---------------------------------------------------------------------- */
CHOLMOD(allocate_work) (nrow, 0, 0, Common) ;
if (Common->status < CHOLMOD_OK)
{
return (FALSE) ;
}
/* ---------------------------------------------------------------------- */
/* order the matrix (does not affect A->p or A->i) */
/* ---------------------------------------------------------------------- */
perm = Common->Head ; /* size nrow+1 (i/l/l) */
/* get parameters */
#ifdef LONG
ccolamd_l_set_defaults (knobs) ;
#else
ccolamd_set_defaults (knobs) ;
#endif
if (Common->current >= 0 && Common->current < CHOLMOD_MAXMETHODS)
{
/* get the knobs from the Common parameters */
knobs [CCOLAMD_DENSE_ROW] =Common->method[Common->current].prune_dense ;
knobs [CCOLAMD_AGGRESSIVE]=Common->method[Common->current].aggressive ;
}
{
#ifdef LONG
csymamd_l (nrow, A->i, A->p, perm, knobs, stats, Common->calloc_memory,
Common->free_memory, Cmember, A->stype) ;
#else
csymamd (nrow, A->i, A->p, perm, knobs, stats, Common->calloc_memory,
Common->free_memory, Cmember, A->stype) ;
#endif
ok = stats [CCOLAMD_STATUS] ;
}
if (ok == CCOLAMD_ERROR_out_of_memory)
{
ERROR (CHOLMOD_OUT_OF_MEMORY, "out of memory") ;
}
ok = (ok == CCOLAMD_OK || ok == CCOLAMD_OK_BUT_JUMBLED) ;
/* ---------------------------------------------------------------------- */
/* free the workspace and return result */
/* ---------------------------------------------------------------------- */
/* permutation returned in perm [0..n-1] */
for (i = 0 ; i < nrow ; i++)
{
Perm [i] = perm [i] ;
}
/* clear Head workspace (used for perm, in csymamd): */
Head = Common->Head ;
for (i = 0 ; i <= nrow ; i++)
{
Head [i] = EMPTY ;
}
return (ok) ;
}
void mexFunction
(
/* === Parameters ======================================================= */
int nargout, /* number of left-hand sides */
mxArray *pargout [ ], /* left-hand side matrices */
int nargin, /* number of right--hand sides */
const mxArray *pargin [ ] /* 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 [CCOLAMD_KNOBS] ; /* ccolamd 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 [CCOLAMD_STATS] ;/* stats for csymamd */
Long *cp, *cp_end, result, nnz, col, length, ok ;
Long *stats ;
stats = stats2 ;
/* === Check inputs ===================================================== */
if (nargin != 3 || nargout > 2)
{
mexErrMsgTxt (
"csymamdtest: incorrect number of input and/or output arguments.") ;
}
/* for testing we require all 4 knobs */
if (mxGetNumberOfElements (pargin [1]) != 4)
{
mexErrMsgTxt ("csymamdtest: must have 4 knobs for testing") ;
}
/* === Get knobs ======================================================== */
ccolamd_l_set_defaults (knobs) ;
spumoni = 0 ;
in_knobs = mxGetPr (pargin [1]) ;
i = mxGetNumberOfElements (pargin [1]) ;
knobs [CCOLAMD_DENSE_ROW] = in_knobs [0] ;
knobs [CCOLAMD_DENSE_COL] = in_knobs [0] ;
knobs [CCOLAMD_AGGRESSIVE] = (in_knobs [1] != 0) ;
spumoni = (in_knobs [2] != 0) ;
/* print knob settings if spumoni is set */
if (spumoni)
{
mexPrintf ("\ncsymamd version %d.%d, %s:\n",
CCOLAMD_MAIN_VERSION, CCOLAMD_SUB_VERSION, CCOLAMD_DATE) ;
if (knobs [CCOLAMD_DENSE_ROW] >= 0)
{
mexPrintf ("knobs(1): %g, rows/cols with > "
"max(16,%g*sqrt(size(A,2))) entries removed\n",
in_knobs [0], knobs [CCOLAMD_DENSE_ROW]) ;
}
else
{
mexPrintf ("knobs(1): %g, no dense rows removed\n",
in_knobs [0]) ;
}
mexPrintf ("knobs(2): %g, aggressive absorption: %s\n",
in_knobs [1], (knobs [CCOLAMD_AGGRESSIVE] != 0) ? "yes" : "no") ;
mexPrintf ("knobs(3): %g, statistics and knobs printed\n",
in_knobs [2]) ;
mexPrintf ("Testing: %g\n", in_knobs [3]) ;
}
/* === If A is full, convert to a sparse matrix ========================= */
Ainput = (mxArray *) pargin [0] ;
if (mxGetNumberOfDimensions (Ainput) != 2)
{
mexErrMsgTxt ("csymamd: input matrix must be 2-dimensional.") ;
}
full = !mxIsSparse (Ainput) ;
if (full)
{
mexCallMATLAB (1, &Ainput, 1, (mxArray **) pargin, "sparse") ;
}
/* === Allocate workspace for csymamd =================================== */
/* get size of matrix */
n_row = mxGetM (Ainput) ;
n_col = mxGetN (Ainput) ;
if (n_col != n_row)
{
mexErrMsgTxt ("csymamd: 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)
{
mexPrintf ("csymamdtest: 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 [4] 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 [3])
{
case 0 :
if (spumoni)
{
mexPrintf ("csymamdtest: no errors expected\n") ;
}
result = 1 ; /* no errors */
break ;
case 1 :
if (spumoni)
{
mexPrintf ("csymamdtest: no errors expected (1)\n") ;
}
result = 1 ;
break ;
case 2 :
if (spumoni)
{
mexPrintf ("csymamdtest: p [0] nonzero\n") ;
}
result = 0 ; /* p [0] must be zero */
p [0] = 1 ;
break ;
case 3 :
if (spumoni)
{
mexPrintf ("csymamdtest: negative length last column\n") ;
}
result = (n_col == 0) ; /* p must be monotonically inc. */
p [n_col] = p [0] ;
break ;
case 4 :
if (spumoni)
{
mexPrintf ("csymamdtest: no errors expected (4)\n") ;
}
result = 1 ;
break ;
case 5 :
if (spumoni)
{
mexPrintf ("csymamdtest: row index out of range (-1)\n") ;
}
if (nnz > 0) /* row index out of range */
{
result = 0 ;
A [nnz-1] = -1 ;
}
else
{
if (spumoni)
{
mexPrintf ("Note: no row indices to put out of range\n") ;
}
result = 1 ;
}
break ;
case 6 :
if (spumoni)
{
mexPrintf ("csymamdtest: 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)
{
mexPrintf ("Note: no row indices to put out of range\n") ;
}
result = 1 ;
}
break ;
case 7 :
if (spumoni)
{
mexPrintf ("csymamdtest: A not present\n") ;
}
result = 0 ; /* A not present */
A = (Long *) NULL ;
break ;
case 8 :
if (spumoni)
{
mexPrintf ("csymamdtest: p not present\n") ;
}
result = 0 ; /* p not present */
p = (Long *) NULL ;
break ;
case 9 :
if (spumoni)
{
mexPrintf ("csymamdtest: 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)
{
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)
{
mexPrintf ("csymamdtest: 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)
{
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)
{
mexPrintf ("csymamdtest: 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)
{
mexPrintf ("csymamdtest: stats not present\n") ;
}
result = 0 ; /* stats not present */
stats = (Long *) NULL ;
break ;
case 13 :
if (spumoni)
{
mexPrintf ("csymamdtest: 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) ============= */
ok = csymamd_l (n_col, A, p, perm, knobs, stats, &mxCalloc, &mxFree,
NULL, -1) ;
if (full)
{
mxDestroyArray (Ainput) ;
}
if (spumoni)
{
csymamd_l_report (stats) ;
}
/* === Return the stats vector ========================================== */
if (nargout == 2)
{
pargout [1] = mxCreateDoubleMatrix (1, CCOLAMD_STATS, mxREAL) ;
out_stats = mxGetPr (pargout [1]) ;
for (i = 0 ; i < CCOLAMD_STATS ; i++)
{
out_stats [i] = (stats == NULL) ? (-1) : (stats [i]) ;
}
/* fix stats (5) and (6), for 1-based information on jumbled matrix. */
/* note that this correction doesn't occur if csymamd returns FALSE */
out_stats [CCOLAMD_INFO1] ++ ;
out_stats [CCOLAMD_INFO2] ++ ;
}
mxFree (A) ;
if (ok)
{
/* === Return the permutation vector ================================ */
pargout [0] = mxCreateDoubleMatrix (1, n_col, mxREAL) ;
out_perm = mxGetPr (pargout [0]) ;
for (i = 0 ; i < n_col ; i++)
{
/* csymamd is 0-based, but MATLAB expects this to be 1-based */
out_perm [i] = perm [i] + 1 ;
}
if (!result)
{
csymamd_l_report (stats) ;
mexErrMsgTxt ("csymamd should have returned TRUE\n") ;
}
}
else
{
/* return p = -1 if csymamd failed */
pargout [0] = mxCreateDoubleMatrix (1, 1, mxREAL) ;
out_perm = mxGetPr (pargout [0]) ;
out_perm [0] = -1 ;
if (result)
{
csymamd_l_report (stats) ;
mexErrMsgTxt ("csymamd should have returned FALSE\n") ;
}
}
mxFree (p) ;
mxFree (perm) ;
}
void mexFunction
(
/* === Parameters ======================================================= */
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
/* === Local variables ================================================== */
Long *A ; /* row indices of input matrix A */
Long *perm ; /* column ordering of M and ordering of A */
Long *cmember ; /* csymamd's copy of the constraint set */
double *in_cmember ; /* input constraint set */
Long *p ; /* column pointers of input matrix A */
Long cslen ; /* size of constraint set */
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 [CCOLAMD_KNOBS] ; /* csymamd 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 [CCOLAMD_STATS] ;/* stats for symamd */
/* === Check inputs ===================================================== */
if (nargin < 1 || nargin > 3 || nargout < 0 || nargout > 2)
{
mexErrMsgTxt ("Usage: [p stats] = csymamd (S, knobs, cmember)") ;
}
/* === Get cmember ====================================================== */
cmember = NULL ;
cslen = 0 ;
if (nargin > 2)
{
in_cmember = mxGetPr (pargin [2]) ;
cslen = mxGetNumberOfElements (pargin [2]) ;
if (cslen != 0)
{
cmember = (Long *) mxCalloc (cslen, sizeof (Long)) ;
for (i = 0 ; i < cslen ; i++)
{
/* convert cmember from 1-based to 0-based */
cmember[i] = ((Long) in_cmember [i] - 1) ;
}
}
}
/* === Get knobs ======================================================== */
ccolamd_l_set_defaults (knobs) ;
spumoni = 0 ;
/* check for user-passed knobs */
i = 0 ;
if (nargin > 1)
{
in_knobs = mxGetPr (pargin [1]) ;
i = mxGetNumberOfElements (pargin [1]) ;
if (i > 0) knobs [CCOLAMD_DENSE_ROW] = in_knobs [0] ;
if (i > 1) knobs [CCOLAMD_AGGRESSIVE] = in_knobs [1] ;
if (i > 2) spumoni = (in_knobs [2] != 0) ;
}
/* print knob settings if spumoni is set */
if (spumoni)
{
mexPrintf ("\ncsymamd version %d.%d, %s:\n",
CCOLAMD_MAIN_VERSION, CCOLAMD_SUB_VERSION, CCOLAMD_DATE) ;
if (knobs [CCOLAMD_DENSE_ROW] >= 0)
{
mexPrintf ("knobs(1): %g, rows/cols with > "
"max(16,%g*sqrt(size(A,2))) entries removed\n",
in_knobs [0], knobs [CCOLAMD_DENSE_ROW]) ;
}
else
{
mexPrintf ("knobs(1): %g, no dense rows removed\n",
in_knobs [0]) ;
}
mexPrintf ("knobs(2): %g, aggressive absorption: %s\n",
in_knobs [1], (knobs [CCOLAMD_AGGRESSIVE] != 0) ? "yes" : "no") ;
mexPrintf ("knobs(3): %g, statistics and knobs printed\n",
in_knobs [2]) ;
}
/* === If A is full, convert to a sparse matrix ========================= */
Ainput = (mxArray *) pargin [0] ;
if (mxGetNumberOfDimensions (Ainput) != 2)
{
mexErrMsgTxt ("csymamd: input matrix must be 2-dimensional.") ;
}
full = !mxIsSparse (Ainput) ;
if (full)
{
mexCallMATLAB (1, &Ainput, 1, (mxArray **) pargin, "sparse") ;
}
/* === Allocate workspace for csymamd =================================== */
/* get size of matrix */
n_row = mxGetM (Ainput) ;
n_col = mxGetN (Ainput) ;
if (n_col != n_row)
{
mexErrMsgTxt ("csymamd: matrix must be square.") ;
}
if (cmember != NULL && cslen != n_col)
{
mexErrMsgTxt ("csymamd: cmember must be of length equal to #cols of A");
}
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 (!csymamd_l (n_col, A, p, perm, knobs, stats, &mxCalloc, &mxFree,
cmember, -1))
{
csymamd_l_report (stats) ;
mexErrMsgTxt ("csymamd error!") ;
}
if (full)
{
mxDestroyArray (Ainput) ;
}
/* === Return the permutation vector ==================================== */
pargout [0] = mxCreateDoubleMatrix (1, n_col, mxREAL) ;
out_perm = mxGetPr (pargout [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) ;
mxFree (cmember) ;
/* === Return the stats vector ========================================== */
/* print stats if spumoni is set */
if (spumoni)
{
csymamd_l_report (stats) ;
}
if (nargout == 2)
{
pargout [1] = mxCreateDoubleMatrix (1, CCOLAMD_STATS, mxREAL) ;
out_stats = mxGetPr (pargout [1]) ;
for (i = 0 ; i < CCOLAMD_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 [CCOLAMD_INFO1] ++ ;
out_stats [CCOLAMD_INFO2] ++ ;
}
}
int main (void)
{
/* ====================================================================== */
/* input matrix A definition */
/* ====================================================================== */
SuiteSparse_long A [ALEN] = {
0, 1, 4, /* row indices of nonzeros in column 0 */
2, 4, /* row indices of nonzeros in column 1 */
0, 1, 2, 3, /* row indices of nonzeros in column 2 */
1, 3} ; /* row indices of nonzeros in column 3 */
SuiteSparse_long p [ ] = {
0, /* column 0 is in A [0..2] */
3, /* column 1 is in A [3..4] */
5, /* column 2 is in A [5..8] */
9, /* column 3 is in A [9..10] */
A_NNZ} ; /* number of nonzeros in A */
/* ====================================================================== */
/* input matrix B definition */
/* ====================================================================== */
SuiteSparse_long B [ ] = { /* Note: only strictly lower triangular part */
/* is included, since symamd ignores the */
/* diagonal and upper triangular part of B. */
1, /* row indices of nonzeros in column 0 */
2, 3, /* row indices of nonzeros in column 1 */
/* row indices of nonzeros in column 2 (none) */
4 /* row indices of nonzeros in column 3 */
} ; /* row indices of nonzeros in column 4 (none) */
SuiteSparse_long q [ ] = {
0, /* column 0 is in B [0] */
1, /* column 1 is in B [1..2] */
3, /* column 2 is empty */
3, /* column 3 is in B [3] */
4, /* column 4 is empty */
B_NNZ} ; /* number of nonzeros in strictly lower B */
/* ====================================================================== */
/* other variable definitions */
/* ====================================================================== */
SuiteSparse_long perm [B_N+1] ; /* note the size is N+1 */
SuiteSparse_long stats [CCOLAMD_STATS] ; /* ccolamd/csymamd output stats */
SuiteSparse_long row, col, pp, length, ok ;
/* ====================================================================== */
/* dump the input matrix A */
/* ====================================================================== */
printf ("ccolamd %d-by-%d input matrix:\n", A_NROW, A_NCOL) ;
for (col = 0 ; col < A_NCOL ; col++)
{
length = p [col+1] - p [col] ;
printf ("Column %ld, with %ld entries:\n", col, length) ;
for (pp = p [col] ; pp < p [col+1] ; pp++)
{
row = A [pp] ;
printf (" row %ld\n", row) ;
}
}
/* ====================================================================== */
/* order the matrix. Note that this destroys A and overwrites p */
/* ====================================================================== */
ok = ccolamd_l (A_NROW, A_NCOL, ALEN, A, p, (double *) NULL, stats, NULL) ;
ccolamd_l_report (stats) ;
if (!ok)
{
printf ("ccolamd error!\n") ;
exit (1) ;
}
/* ====================================================================== */
/* print the column ordering */
/* ====================================================================== */
printf ("ccolamd_l column ordering:\n") ;
printf ("1st column: %ld\n", p [0]) ;
printf ("2nd column: %ld\n", p [1]) ;
printf ("3rd column: %ld\n", p [2]) ;
printf ("4th column: %ld\n", p [3]) ;
/* ====================================================================== */
/* dump the strictly lower triangular part of symmetric input matrix B */
/* ====================================================================== */
printf ("\n\ncsymamd_l %d-by-%d input matrix:\n", B_N, B_N) ;
printf ("Entries in strictly lower triangular part:\n") ;
for (col = 0 ; col < B_N ; col++)
{
length = q [col+1] - q [col] ;
printf ("Column %ld, with %ld entries:\n", col, length) ;
for (pp = q [col] ; pp < q [col+1] ; pp++)
{
row = B [pp] ;
printf (" row %ld\n", row) ;
}
}
/* ====================================================================== */
/* order the matrix B. Note that this does not modify B or q. */
/* ====================================================================== */
ok = csymamd_l (B_N, B, q, perm, (double *) NULL, stats, &calloc, &free,
NULL, -1) ;
csymamd_l_report (stats) ;
if (!ok)
{
printf ("csymamd error!\n") ;
exit (1) ;
}
/* ====================================================================== */
/* print the symmetric ordering */
/* ====================================================================== */
printf ("csymamd_l column ordering:\n") ;
printf ("1st row/column: %ld\n", perm [0]) ;
printf ("2nd row/column: %ld\n", perm [1]) ;
printf ("3rd row/column: %ld\n", perm [2]) ;
printf ("4th row/column: %ld\n", perm [3]) ;
printf ("5th row/column: %ld\n", perm [4]) ;
return (0) ;
}
