sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.19__cp310-cp310-win_amd64.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h

@@ -1,1863 +0,0 @@
-// // This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Desire Nuentsa Wakam <desire.nuentsa_wakam@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-// This file is modified from the colamd/symamd library. The copyright is below
-
-//   The authors of the code itself are Stefan I. Larimore and Timothy A.
-//   Davis (davis@cise.ufl.edu), University of Florida.  The algorithm was
-//   developed in collaboration with John Gilbert, Xerox PARC, and Esmond
-//   Ng, Oak Ridge National Laboratory.
-//
-//     Date:
-//
-//   September 8, 2003.  Version 2.3.
-//
-//     Acknowledgements:
-//
-//   This work was supported by the National Science Foundation, under
-//   grants DMS-9504974 and DMS-9803599.
-//
-//     Notice:
-//
-//   Copyright (c) 1998-2003 by the University of Florida.
-//   All Rights Reserved.
-//
-//   THIS MATERIAL IS PROVIDED AS IS, WITH ABSOLUTELY NO WARRANTY
-//   EXPRESSED OR IMPLIED.  ANY USE IS AT YOUR OWN RISK.
-//
-//   Permission is hereby granted to use, copy, modify, and/or distribute
-//   this program, provided that the Copyright, this License, and the
-//   Availability of the original version is retained on all copies and made
-//   accessible to the end-user of any code or package that includes COLAMD
-//   or any modified version of COLAMD.
-//
-//     Availability:
-//
-//   The colamd/symamd library is available at
-//
-//       http://www.suitesparse.com
-
-
-#ifndef EIGEN_COLAMD_H
-#define EIGEN_COLAMD_H
-
-namespace internal {
-
-namespace Colamd {
-
-/* Ensure that debugging is turned off: */
-#ifndef COLAMD_NDEBUG
-#define COLAMD_NDEBUG
-#endif /* NDEBUG */
-
-
-/* ========================================================================== */
-/* === Knob and statistics definitions ====================================== */
-/* ========================================================================== */
-
-/* size of the knobs [ ] array.  Only knobs [0..1] are currently used. */
-const int NKnobs = 20;
-
-/* number of output statistics.  Only stats [0..6] are currently used. */
-const int NStats = 20;
-
-/* Indices into knobs and stats array. */
-enum KnobsStatsIndex {
-  /* knobs [0] and stats [0]: dense row knob and output statistic. */
-  DenseRow = 0,
-
-  /* knobs [1] and stats [1]: dense column knob and output statistic. */
-  DenseCol = 1,
-
-  /* stats [2]: memory defragmentation count output statistic */
-  DefragCount = 2,
-
-  /* stats [3]: colamd status:  zero OK, > 0 warning or notice, < 0 error */
-  Status = 3,
-
-  /* stats [4..6]: error info, or info on jumbled columns */
-  Info1 = 4,
-  Info2 = 5,
-  Info3 = 6
-};
-
-/* error codes returned in stats [3]: */
-enum Status {
-  Ok = 0,
-  OkButJumbled = 1,
-  ErrorANotPresent = -1,
-  ErrorPNotPresent = -2,
-  ErrorNrowNegative = -3,
-  ErrorNcolNegative = -4,
-  ErrorNnzNegative = -5,
-  ErrorP0Nonzero = -6,
-  ErrorATooSmall = -7,
-  ErrorColLengthNegative = -8,
-  ErrorRowIndexOutOfBounds = -9,
-  ErrorOutOfMemory = -10,
-  ErrorInternalError = -999
-};
-/* ========================================================================== */
-/* === Definitions ========================================================== */
-/* ========================================================================== */
-
-template <typename IndexType>
-IndexType ones_complement(const IndexType r) {
-  return (-(r)-1);
-}
-
-/* -------------------------------------------------------------------------- */
-const int Empty = -1;
-
-/* Row and column status */
-enum RowColumnStatus {
-  Alive = 0,
-  Dead = -1
-};
-
-/* Column status */
-enum ColumnStatus {
-  DeadPrincipal = -1,
-  DeadNonPrincipal = -2
-};
-
-/* ========================================================================== */
-/* === Colamd reporting mechanism =========================================== */
-/* ========================================================================== */
-
-// == Row and Column structures ==
-template <typename IndexType>
-struct ColStructure
-{
-  IndexType start ;   /* index for A of first row in this column, or Dead */
-  /* if column is dead */
-  IndexType length ;  /* number of rows in this column */
-  union
-  {
-    IndexType thickness ; /* number of original columns represented by this */
-    /* col, if the column is alive */
-    IndexType parent ;  /* parent in parent tree super-column structure, if */
-    /* the column is dead */
-  } shared1 ;
-  union
-  {
-    IndexType score ; /* the score used to maintain heap, if col is alive */
-    IndexType order ; /* pivot ordering of this column, if col is dead */
-  } shared2 ;
-  union
-  {
-    IndexType headhash ;  /* head of a hash bucket, if col is at the head of */
-    /* a degree list */
-    IndexType hash ;  /* hash value, if col is not in a degree list */
-    IndexType prev ;  /* previous column in degree list, if col is in a */
-    /* degree list (but not at the head of a degree list) */
-  } shared3 ;
-  union
-  {
-    IndexType degree_next ; /* next column, if col is in a degree list */
-    IndexType hash_next ;   /* next column, if col is in a hash list */
-  } shared4 ;
-
-  inline bool is_dead() const { return start < Alive; }
-
-  inline bool is_alive() const { return start >= Alive; }
-
-  inline bool is_dead_principal() const { return start == DeadPrincipal; }
-
-  inline void kill_principal() { start = DeadPrincipal; }
-
-  inline void kill_non_principal() { start = DeadNonPrincipal; }
-
-};
-
-template <typename IndexType>
-struct RowStructure
-{
-  IndexType start ;   /* index for A of first col in this row */
-  IndexType length ;  /* number of principal columns in this row */
-  union
-  {
-    IndexType degree ;  /* number of principal & non-principal columns in row */
-    IndexType p ;   /* used as a row pointer in init_rows_cols () */
-  } shared1 ;
-  union
-  {
-    IndexType mark ;  /* for computing set differences and marking dead rows*/
-    IndexType first_column ;/* first column in row (used in garbage collection) */
-  } shared2 ;
-
-  inline bool is_dead() const { return shared2.mark < Alive; }
-
-  inline bool is_alive() const { return shared2.mark >= Alive; }
-
-  inline void kill() { shared2.mark = Dead; }
-
-};
-
-/* ========================================================================== */
-/* === Colamd recommended memory size ======================================= */
-/* ========================================================================== */
-
-/*
-  The recommended length Alen of the array A passed to colamd is given by
-  the COLAMD_RECOMMENDED (nnz, n_row, n_col) macro.  It returns -1 if any
-  argument is negative.  2*nnz space is required for the row and column
-  indices of the matrix. colamd_c (n_col) + colamd_r (n_row) space is
-  required for the Col and Row arrays, respectively, which are internal to
-  colamd.  An additional n_col space is the minimal amount of "elbow room",
-  and nnz/5 more space is recommended for run time efficiency.
-
-  This macro is not needed when using symamd.
-
-  Explicit typecast to IndexType added Sept. 23, 2002, COLAMD version 2.2, to avoid
-  gcc -pedantic warning messages.
-*/
-template <typename IndexType>
-inline IndexType colamd_c(IndexType n_col)
-{ return IndexType( ((n_col) + 1) * sizeof (ColStructure<IndexType>) / sizeof (IndexType) ) ; }
-
-template <typename IndexType>
-inline IndexType  colamd_r(IndexType n_row)
-{ return IndexType(((n_row) + 1) * sizeof (RowStructure<IndexType>) / sizeof (IndexType)); }
-
-// Prototypes of non-user callable routines
-template <typename IndexType>
-static IndexType init_rows_cols (IndexType n_row, IndexType n_col, RowStructure<IndexType> Row [], ColStructure<IndexType> col [], IndexType A [], IndexType p [], IndexType stats[NStats] );
-
-template <typename IndexType>
-static void init_scoring (IndexType n_row, IndexType n_col, RowStructure<IndexType> Row [], ColStructure<IndexType> Col [], IndexType A [], IndexType head [], double knobs[NKnobs], IndexType *p_n_row2, IndexType *p_n_col2, IndexType *p_max_deg);
-
-template <typename IndexType>
-static IndexType find_ordering (IndexType n_row, IndexType n_col, IndexType Alen, RowStructure<IndexType> Row [], ColStructure<IndexType> Col [], IndexType A [], IndexType head [], IndexType n_col2, IndexType max_deg, IndexType pfree);
-
-template <typename IndexType>
-static void order_children (IndexType n_col, ColStructure<IndexType> Col [], IndexType p []);
-
-template <typename IndexType>
-static void detect_super_cols (ColStructure<IndexType> Col [], IndexType A [], IndexType head [], IndexType row_start, IndexType row_length ) ;
-
-template <typename IndexType>
-static IndexType garbage_collection (IndexType n_row, IndexType n_col, RowStructure<IndexType> Row [], ColStructure<IndexType> Col [], IndexType A [], IndexType *pfree) ;
-
-template <typename IndexType>
-static inline  IndexType clear_mark (IndexType n_row, RowStructure<IndexType> Row [] ) ;
-
-/* === No debugging ========================================================= */
-
-#define COLAMD_DEBUG0(params) ;
-#define COLAMD_DEBUG1(params) ;
-#define COLAMD_DEBUG2(params) ;
-#define COLAMD_DEBUG3(params) ;
-#define COLAMD_DEBUG4(params) ;
-
-#define COLAMD_ASSERT(expression) ((void) 0)
-
-
-/**
- * \brief Returns the recommended value of Alen
- *
- * Returns recommended value of Alen for use by colamd.
- * Returns -1 if any input argument is negative.
- * The use of this routine or macro is optional.
- * Note that the macro uses its arguments   more than once,
- * so be careful for side effects, if you pass expressions as arguments to COLAMD_RECOMMENDED.
- *
- * \param nnz nonzeros in A
- * \param n_row number of rows in A
- * \param n_col number of columns in A
- * \return recommended value of Alen for use by colamd
- */
-template <typename IndexType>
-inline IndexType recommended ( IndexType nnz, IndexType n_row, IndexType n_col)
-{
-  if ((nnz) < 0 || (n_row) < 0 || (n_col) < 0)
-    return (-1);
-  else
-    return (2 * (nnz) + colamd_c (n_col) + colamd_r (n_row) + (n_col) + ((nnz) / 5));
-}
-
-/**
- * \brief set default parameters  The use of this routine is optional.
- *
- * Colamd: rows with more than (knobs [DenseRow] * n_col)
- * entries are removed prior to ordering.  Columns with more than
- * (knobs [DenseCol] * n_row) entries are removed prior to
- * ordering, and placed last in the output column ordering.
- *
- * DenseRow and DenseCol are defined as 0 and 1,
- * respectively, in colamd.h.  Default values of these two knobs
- * are both 0.5.  Currently, only knobs [0] and knobs [1] are
- * used, but future versions may use more knobs.  If so, they will
- * be properly set to their defaults by the future version of
- * colamd_set_defaults, so that the code that calls colamd will
- * not need to change, assuming that you either use
- * colamd_set_defaults, or pass a (double *) NULL pointer as the
- * knobs array to colamd or symamd.
- *
- * \param knobs parameter settings for colamd
- */
-
-static inline void set_defaults(double knobs[NKnobs])
-{
-  /* === Local variables ================================================== */
-
-  int i ;
-
-  if (!knobs)
-  {
-    return ;      /* no knobs to initialize */
-  }
-  for (i = 0 ; i < NKnobs ; i++)
-  {
-    knobs [i] = 0 ;
-  }
-  knobs [Colamd::DenseRow] = 0.5 ;  /* ignore rows over 50% dense */
-  knobs [Colamd::DenseCol] = 0.5 ;  /* ignore columns over 50% dense */
-}
-
-/**
- * \brief  Computes a column ordering using the column approximate minimum degree ordering
- *
- * Computes a column ordering (Q) of A such that P(AQ)=LU or
- * (AQ)'AQ=LL' have less fill-in and require fewer floating point
- * operations than factorizing the unpermuted matrix A or A'A,
- * respectively.
- *
- *
- * \param n_row number of rows in A
- * \param n_col number of columns in A
- * \param Alen, size of the array A
- * \param A row indices of the matrix, of size ALen
- * \param p column pointers of A, of size n_col+1
- * \param knobs parameter settings for colamd
- * \param stats colamd output statistics and error codes
- */
-template <typename IndexType>
-static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats])
-{
-  /* === Local variables ================================================== */
-
-  IndexType i ;     /* loop index */
-  IndexType nnz ;     /* nonzeros in A */
-  IndexType Row_size ;    /* size of Row [], in integers */
-  IndexType Col_size ;    /* size of Col [], in integers */
-  IndexType need ;      /* minimum required length of A */
-  Colamd::RowStructure<IndexType> *Row ;   /* pointer into A of Row [0..n_row] array */
-  Colamd::ColStructure<IndexType> *Col ;   /* pointer into A of Col [0..n_col] array */
-  IndexType n_col2 ;    /* number of non-dense, non-empty columns */
-  IndexType n_row2 ;    /* number of non-dense, non-empty rows */
-  IndexType ngarbage ;    /* number of garbage collections performed */
-  IndexType max_deg ;   /* maximum row degree */
-  double default_knobs [NKnobs] ; /* default knobs array */
-
-
-  /* === Check the input arguments ======================================== */
-
-  if (!stats)
-  {
-    COLAMD_DEBUG0 (("colamd: stats not present\n")) ;
-    return (false) ;
-  }
-  for (i = 0 ; i < NStats ; i++)
-  {
-    stats [i] = 0 ;
-  }
-  stats [Colamd::Status] = Colamd::Ok ;
-  stats [Colamd::Info1] = -1 ;
-  stats [Colamd::Info2] = -1 ;
-
-  if (!A)   /* A is not present */
-  {
-    stats [Colamd::Status] = Colamd::ErrorANotPresent ;
-    COLAMD_DEBUG0 (("colamd: A not present\n")) ;
-    return (false) ;
-  }
-
-  if (!p)   /* p is not present */
-  {
-    stats [Colamd::Status] = Colamd::ErrorPNotPresent ;
-    COLAMD_DEBUG0 (("colamd: p not present\n")) ;
-    return (false) ;
-  }
-
-  if (n_row < 0)  /* n_row must be >= 0 */
-  {
-    stats [Colamd::Status] = Colamd::ErrorNrowNegative ;
-    stats [Colamd::Info1] = n_row ;
-    COLAMD_DEBUG0 (("colamd: nrow negative %d\n", n_row)) ;
-    return (false) ;
-  }
-
-  if (n_col < 0)  /* n_col must be >= 0 */
-  {
-    stats [Colamd::Status] = Colamd::ErrorNcolNegative ;
-    stats [Colamd::Info1] = n_col ;
-    COLAMD_DEBUG0 (("colamd: ncol negative %d\n", n_col)) ;
-    return (false) ;
-  }
-
-  nnz = p [n_col] ;
-  if (nnz < 0)  /* nnz must be >= 0 */
-  {
-    stats [Colamd::Status] = Colamd::ErrorNnzNegative ;
-    stats [Colamd::Info1] = nnz ;
-    COLAMD_DEBUG0 (("colamd: number of entries negative %d\n", nnz)) ;
-    return (false) ;
-  }
-
-  if (p [0] != 0)
-  {
-    stats [Colamd::Status] = Colamd::ErrorP0Nonzero ;
-    stats [Colamd::Info1] = p [0] ;
-    COLAMD_DEBUG0 (("colamd: p[0] not zero %d\n", p [0])) ;
-    return (false) ;
-  }
-
-  /* === If no knobs, set default knobs =================================== */
-
-  if (!knobs)
-  {
-    set_defaults (default_knobs) ;
-    knobs = default_knobs ;
-  }
-
-  /* === Allocate the Row and Col arrays from array A ===================== */
-
-  Col_size = colamd_c (n_col) ;
-  Row_size = colamd_r (n_row) ;
-  need = 2*nnz + n_col + Col_size + Row_size ;
-
-  if (need > Alen)
-  {
-    /* not enough space in array A to perform the ordering */
-    stats [Colamd::Status] = Colamd::ErrorATooSmall ;
-    stats [Colamd::Info1] = need ;
-    stats [Colamd::Info2] = Alen ;
-    COLAMD_DEBUG0 (("colamd: Need Alen >= %d, given only Alen = %d\n", need,Alen));
-    return (false) ;
-  }
-
-  Alen -= Col_size + Row_size ;
-  Col = (ColStructure<IndexType> *) &A [Alen] ;
-  Row = (RowStructure<IndexType> *) &A [Alen + Col_size] ;
-
-  /* === Construct the row and column data structures ===================== */
-
-  if (!Colamd::init_rows_cols (n_row, n_col, Row, Col, A, p, stats))
-  {
-    /* input matrix is invalid */
-    COLAMD_DEBUG0 (("colamd: Matrix invalid\n")) ;
-    return (false) ;
-  }
-
-  /* === Initialize scores, kill dense rows/columns ======================= */
-
-  Colamd::init_scoring (n_row, n_col, Row, Col, A, p, knobs,
-		&n_row2, &n_col2, &max_deg) ;
-
-  /* === Order the supercolumns =========================================== */
-
-  ngarbage = Colamd::find_ordering (n_row, n_col, Alen, Row, Col, A, p,
-			    n_col2, max_deg, 2*nnz) ;
-
-  /* === Order the non-principal columns ================================== */
-
-  Colamd::order_children (n_col, Col, p) ;
-
-  /* === Return statistics in stats ======================================= */
-
-  stats [Colamd::DenseRow] = n_row - n_row2 ;
-  stats [Colamd::DenseCol] = n_col - n_col2 ;
-  stats [Colamd::DefragCount] = ngarbage ;
-  COLAMD_DEBUG0 (("colamd: done.\n")) ;
-  return (true) ;
-}
-
-/* ========================================================================== */
-/* === NON-USER-CALLABLE ROUTINES: ========================================== */
-/* ========================================================================== */
-
-/* There are no user-callable routines beyond this point in the file */
-
-/* ========================================================================== */
-/* === init_rows_cols ======================================================= */
-/* ========================================================================== */
-
-/*
-  Takes the column form of the matrix in A and creates the row form of the
-  matrix.  Also, row and column attributes are stored in the Col and Row
-  structs.  If the columns are un-sorted or contain duplicate row indices,
-  this routine will also sort and remove duplicate row indices from the
-  column form of the matrix.  Returns false if the matrix is invalid,
-  true otherwise.  Not user-callable.
-*/
-template <typename IndexType>
-static IndexType init_rows_cols  /* returns true if OK, or false otherwise */
-  (
-    /* === Parameters ======================================================= */
-
-    IndexType n_row,      /* number of rows of A */
-    IndexType n_col,      /* number of columns of A */
-    RowStructure<IndexType> Row [],    /* of size n_row+1 */
-    ColStructure<IndexType> Col [],    /* of size n_col+1 */
-    IndexType A [],     /* row indices of A, of size Alen */
-    IndexType p [],     /* pointers to columns in A, of size n_col+1 */
-    IndexType stats [NStats]  /* colamd statistics */
-    )
-{
-  /* === Local variables ================================================== */
-
-  IndexType col ;     /* a column index */
-  IndexType row ;     /* a row index */
-  IndexType *cp ;     /* a column pointer */
-  IndexType *cp_end ;   /* a pointer to the end of a column */
-  IndexType *rp ;     /* a row pointer */
-  IndexType *rp_end ;   /* a pointer to the end of a row */
-  IndexType last_row ;    /* previous row */
-
-  /* === Initialize columns, and check column pointers ==================== */
-
-  for (col = 0 ; col < n_col ; col++)
-  {
-    Col [col].start = p [col] ;
-    Col [col].length = p [col+1] - p [col] ;
-
-    if ((Col [col].length) < 0) // extra parentheses to work-around gcc bug 10200
-    {
-      /* column pointers must be non-decreasing */
-      stats [Colamd::Status] = Colamd::ErrorColLengthNegative ;
-      stats [Colamd::Info1] = col ;
-      stats [Colamd::Info2] = Col [col].length ;
-      COLAMD_DEBUG0 (("colamd: col %d length %d < 0\n", col, Col [col].length)) ;
-      return (false) ;
-    }
-
-    Col [col].shared1.thickness = 1 ;
-    Col [col].shared2.score = 0 ;
-    Col [col].shared3.prev = Empty ;
-    Col [col].shared4.degree_next = Empty ;
-  }
-
-  /* p [0..n_col] no longer needed, used as "head" in subsequent routines */
-
-  /* === Scan columns, compute row degrees, and check row indices ========= */
-
-  stats [Info3] = 0 ;  /* number of duplicate or unsorted row indices*/
-
-  for (row = 0 ; row < n_row ; row++)
-  {
-    Row [row].length = 0 ;
-    Row [row].shared2.mark = -1 ;
-  }
-
-  for (col = 0 ; col < n_col ; col++)
-  {
-    last_row = -1 ;
-
-    cp = &A [p [col]] ;
-    cp_end = &A [p [col+1]] ;
-
-    while (cp < cp_end)
-    {
-      row = *cp++ ;
-
-      /* make sure row indices within range */
-      if (row < 0 || row >= n_row)
-      {
-	stats [Colamd::Status] = Colamd::ErrorRowIndexOutOfBounds ;
-	stats [Colamd::Info1] = col ;
-	stats [Colamd::Info2] = row ;
-	stats [Colamd::Info3] = n_row ;
-	COLAMD_DEBUG0 (("colamd: row %d col %d out of bounds\n", row, col)) ;
-	return (false) ;
-      }
-
-      if (row <= last_row || Row [row].shared2.mark == col)
-      {
-	/* row index are unsorted or repeated (or both), thus col */
-	/* is jumbled.  This is a notice, not an error condition. */
-	stats [Colamd::Status] = Colamd::OkButJumbled ;
-	stats [Colamd::Info1] = col ;
-	stats [Colamd::Info2] = row ;
-	(stats [Colamd::Info3]) ++ ;
-	COLAMD_DEBUG1 (("colamd: row %d col %d unsorted/duplicate\n",row,col));
-      }
-
-      if (Row [row].shared2.mark != col)
-      {
-	Row [row].length++ ;
-      }
-      else
-      {
-	/* this is a repeated entry in the column, */
-	/* it will be removed */
-	Col [col].length-- ;
-      }
-
-      /* mark the row as having been seen in this column */
-      Row [row].shared2.mark = col ;
-
-      last_row = row ;
-    }
-  }
-
-  /* === Compute row pointers ============================================= */
-
-  /* row form of the matrix starts directly after the column */
-  /* form of matrix in A */
-  Row [0].start = p [n_col] ;
-  Row [0].shared1.p = Row [0].start ;
-  Row [0].shared2.mark = -1 ;
-  for (row = 1 ; row < n_row ; row++)
-  {
-    Row [row].start = Row [row-1].start + Row [row-1].length ;
-    Row [row].shared1.p = Row [row].start ;
-    Row [row].shared2.mark = -1 ;
-  }
-
-  /* === Create row form ================================================== */
-
-  if (stats [Status] == OkButJumbled)
-  {
-    /* if cols jumbled, watch for repeated row indices */
-    for (col = 0 ; col < n_col ; col++)
-    {
-      cp = &A [p [col]] ;
-      cp_end = &A [p [col+1]] ;
-      while (cp < cp_end)
-      {
-	row = *cp++ ;
-	if (Row [row].shared2.mark != col)
-	{
-	  A [(Row [row].shared1.p)++] = col ;
-	  Row [row].shared2.mark = col ;
-	}
-      }
-    }
-  }
-  else
-  {
-    /* if cols not jumbled, we don't need the mark (this is faster) */
-    for (col = 0 ; col < n_col ; col++)
-    {
-      cp = &A [p [col]] ;
-      cp_end = &A [p [col+1]] ;
-      while (cp < cp_end)
-      {
-	A [(Row [*cp++].shared1.p)++] = col ;
-      }
-    }
-  }
-
-  /* === Clear the row marks and set row degrees ========================== */
-
-  for (row = 0 ; row < n_row ; row++)
-  {
-    Row [row].shared2.mark = 0 ;
-    Row [row].shared1.degree = Row [row].length ;
-  }
-
-  /* === See if we need to re-create columns ============================== */
-
-  if (stats [Status] == OkButJumbled)
-  {
-    COLAMD_DEBUG0 (("colamd: reconstructing column form, matrix jumbled\n")) ;
-
-
-    /* === Compute col pointers ========================================= */
-
-    /* col form of the matrix starts at A [0]. */
-    /* Note, we may have a gap between the col form and the row */
-    /* form if there were duplicate entries, if so, it will be */
-    /* removed upon the first garbage collection */
-    Col [0].start = 0 ;
-    p [0] = Col [0].start ;
-    for (col = 1 ; col < n_col ; col++)
-    {
-      /* note that the lengths here are for pruned columns, i.e. */
-      /* no duplicate row indices will exist for these columns */
-      Col [col].start = Col [col-1].start + Col [col-1].length ;
-      p [col] = Col [col].start ;
-    }
-
-    /* === Re-create col form =========================================== */
-
-    for (row = 0 ; row < n_row ; row++)
-    {
-      rp = &A [Row [row].start] ;
-      rp_end = rp + Row [row].length ;
-      while (rp < rp_end)
-      {
-	A [(p [*rp++])++] = row ;
-      }
-    }
-  }
-
-  /* === Done.  Matrix is not (or no longer) jumbled ====================== */
-
-  return (true) ;
-}
-
-
-/* ========================================================================== */
-/* === init_scoring ========================================================= */
-/* ========================================================================== */
-
-/*
-  Kills dense or empty columns and rows, calculates an initial score for
-  each column, and places all columns in the degree lists.  Not user-callable.
-*/
-template <typename IndexType>
-static void init_scoring
-  (
-    /* === Parameters ======================================================= */
-
-    IndexType n_row,      /* number of rows of A */
-    IndexType n_col,      /* number of columns of A */
-    RowStructure<IndexType> Row [],    /* of size n_row+1 */
-    ColStructure<IndexType> Col [],    /* of size n_col+1 */
-    IndexType A [],     /* column form and row form of A */
-    IndexType head [],    /* of size n_col+1 */
-    double knobs [NKnobs],/* parameters */
-    IndexType *p_n_row2,    /* number of non-dense, non-empty rows */
-    IndexType *p_n_col2,    /* number of non-dense, non-empty columns */
-    IndexType *p_max_deg    /* maximum row degree */
-    )
-{
-  /* === Local variables ================================================== */
-
-  IndexType c ;     /* a column index */
-  IndexType r, row ;    /* a row index */
-  IndexType *cp ;     /* a column pointer */
-  IndexType deg ;     /* degree of a row or column */
-  IndexType *cp_end ;   /* a pointer to the end of a column */
-  IndexType *new_cp ;   /* new column pointer */
-  IndexType col_length ;    /* length of pruned column */
-  IndexType score ;     /* current column score */
-  IndexType n_col2 ;    /* number of non-dense, non-empty columns */
-  IndexType n_row2 ;    /* number of non-dense, non-empty rows */
-  IndexType dense_row_count ; /* remove rows with more entries than this */
-  IndexType dense_col_count ; /* remove cols with more entries than this */
-  IndexType min_score ;   /* smallest column score */
-  IndexType max_deg ;   /* maximum row degree */
-  IndexType next_col ;    /* Used to add to degree list.*/
-
-
-  /* === Extract knobs ==================================================== */
-
-  dense_row_count = numext::maxi(IndexType(0), numext::mini(IndexType(knobs [Colamd::DenseRow] * n_col), n_col)) ;
-  dense_col_count = numext::maxi(IndexType(0), numext::mini(IndexType(knobs [Colamd::DenseCol] * n_row), n_row)) ;
-  COLAMD_DEBUG1 (("colamd: densecount: %d %d\n", dense_row_count, dense_col_count)) ;
-  max_deg = 0 ;
-  n_col2 = n_col ;
-  n_row2 = n_row ;
-
-  /* === Kill empty columns =============================================== */
-
-  /* Put the empty columns at the end in their natural order, so that LU */
-  /* factorization can proceed as far as possible. */
-  for (c = n_col-1 ; c >= 0 ; c--)
-  {
-    deg = Col [c].length ;
-    if (deg == 0)
-    {
-      /* this is a empty column, kill and order it last */
-      Col [c].shared2.order = --n_col2 ;
-      Col[c].kill_principal() ;
-    }
-  }
-  COLAMD_DEBUG1 (("colamd: null columns killed: %d\n", n_col - n_col2)) ;
-
-  /* === Kill dense columns =============================================== */
-
-  /* Put the dense columns at the end, in their natural order */
-  for (c = n_col-1 ; c >= 0 ; c--)
-  {
-    /* skip any dead columns */
-    if (Col[c].is_dead())
-    {
-      continue ;
-    }
-    deg = Col [c].length ;
-    if (deg > dense_col_count)
-    {
-      /* this is a dense column, kill and order it last */
-      Col [c].shared2.order = --n_col2 ;
-      /* decrement the row degrees */
-      cp = &A [Col [c].start] ;
-      cp_end = cp + Col [c].length ;
-      while (cp < cp_end)
-      {
-	Row [*cp++].shared1.degree-- ;
-      }
-      Col[c].kill_principal() ;
-    }
-  }
-  COLAMD_DEBUG1 (("colamd: Dense and null columns killed: %d\n", n_col - n_col2)) ;
-
-  /* === Kill dense and empty rows ======================================== */
-
-  for (r = 0 ; r < n_row ; r++)
-  {
-    deg = Row [r].shared1.degree ;
-    COLAMD_ASSERT (deg >= 0 && deg <= n_col) ;
-    if (deg > dense_row_count || deg == 0)
-    {
-      /* kill a dense or empty row */
-      Row[r].kill() ;
-      --n_row2 ;
-    }
-    else
-    {
-      /* keep track of max degree of remaining rows */
-      max_deg = numext::maxi(max_deg, deg) ;
-    }
-  }
-  COLAMD_DEBUG1 (("colamd: Dense and null rows killed: %d\n", n_row - n_row2)) ;
-
-  /* === Compute initial column scores ==================================== */
-
-  /* At this point the row degrees are accurate.  They reflect the number */
-  /* of "live" (non-dense) columns in each row.  No empty rows exist. */
-  /* Some "live" columns may contain only dead rows, however.  These are */
-  /* pruned in the code below. */
-
-  /* now find the initial matlab score for each column */
-  for (c = n_col-1 ; c >= 0 ; c--)
-  {
-    /* skip dead column */
-    if (Col[c].is_dead())
-    {
-      continue ;
-    }
-    score = 0 ;
-    cp = &A [Col [c].start] ;
-    new_cp = cp ;
-    cp_end = cp + Col [c].length ;
-    while (cp < cp_end)
-    {
-      /* get a row */
-      row = *cp++ ;
-      /* skip if dead */
-      if (Row[row].is_dead())
-      {
-	continue ;
-      }
-      /* compact the column */
-      *new_cp++ = row ;
-      /* add row's external degree */
-      score += Row [row].shared1.degree - 1 ;
-      /* guard against integer overflow */
-      score = numext::mini(score, n_col) ;
-    }
-    /* determine pruned column length */
-    col_length = (IndexType) (new_cp - &A [Col [c].start]) ;
-    if (col_length == 0)
-    {
-      /* a newly-made null column (all rows in this col are "dense" */
-      /* and have already been killed) */
-      COLAMD_DEBUG2 (("Newly null killed: %d\n", c)) ;
-      Col [c].shared2.order = --n_col2 ;
-      Col[c].kill_principal() ;
-    }
-    else
-    {
-      /* set column length and set score */
-      COLAMD_ASSERT (score >= 0) ;
-      COLAMD_ASSERT (score <= n_col) ;
-      Col [c].length = col_length ;
-      Col [c].shared2.score = score ;
-    }
-  }
-  COLAMD_DEBUG1 (("colamd: Dense, null, and newly-null columns killed: %d\n",
-		  n_col-n_col2)) ;
-
-  /* At this point, all empty rows and columns are dead.  All live columns */
-  /* are "clean" (containing no dead rows) and simplicial (no supercolumns */
-  /* yet).  Rows may contain dead columns, but all live rows contain at */
-  /* least one live column. */
-
-  /* === Initialize degree lists ========================================== */
-
-
-  /* clear the hash buckets */
-  for (c = 0 ; c <= n_col ; c++)
-  {
-    head [c] = Empty ;
-  }
-  min_score = n_col ;
-  /* place in reverse order, so low column indices are at the front */
-  /* of the lists.  This is to encourage natural tie-breaking */
-  for (c = n_col-1 ; c >= 0 ; c--)
-  {
-    /* only add principal columns to degree lists */
-    if (Col[c].is_alive())
-    {
-      COLAMD_DEBUG4 (("place %d score %d minscore %d ncol %d\n",
-		      c, Col [c].shared2.score, min_score, n_col)) ;
-
-      /* === Add columns score to DList =============================== */
-
-      score = Col [c].shared2.score ;
-
-      COLAMD_ASSERT (min_score >= 0) ;
-      COLAMD_ASSERT (min_score <= n_col) ;
-      COLAMD_ASSERT (score >= 0) ;
-      COLAMD_ASSERT (score <= n_col) ;
-      COLAMD_ASSERT (head [score] >= Empty) ;
-
-      /* now add this column to dList at proper score location */
-      next_col = head [score] ;
-      Col [c].shared3.prev = Empty ;
-      Col [c].shared4.degree_next = next_col ;
-
-      /* if there already was a column with the same score, set its */
-      /* previous pointer to this new column */
-      if (next_col != Empty)
-      {
-	Col [next_col].shared3.prev = c ;
-      }
-      head [score] = c ;
-
-      /* see if this score is less than current min */
-      min_score = numext::mini(min_score, score) ;
-
-
-    }
-  }
-
-
-  /* === Return number of remaining columns, and max row degree =========== */
-
-  *p_n_col2 = n_col2 ;
-  *p_n_row2 = n_row2 ;
-  *p_max_deg = max_deg ;
-}
-
-
-/* ========================================================================== */
-/* === find_ordering ======================================================== */
-/* ========================================================================== */
-
-/*
-  Order the principal columns of the supercolumn form of the matrix
-  (no supercolumns on input).  Uses a minimum approximate column minimum
-  degree ordering method.  Not user-callable.
-*/
-template <typename IndexType>
-static IndexType find_ordering /* return the number of garbage collections */
-  (
-    /* === Parameters ======================================================= */
-
-    IndexType n_row,      /* number of rows of A */
-    IndexType n_col,      /* number of columns of A */
-    IndexType Alen,     /* size of A, 2*nnz + n_col or larger */
-    RowStructure<IndexType> Row [],    /* of size n_row+1 */
-    ColStructure<IndexType> Col [],    /* of size n_col+1 */
-    IndexType A [],     /* column form and row form of A */
-    IndexType head [],    /* of size n_col+1 */
-    IndexType n_col2,     /* Remaining columns to order */
-    IndexType max_deg,    /* Maximum row degree */
-    IndexType pfree     /* index of first free slot (2*nnz on entry) */
-    )
-{
-  /* === Local variables ================================================== */
-
-  IndexType k ;     /* current pivot ordering step */
-  IndexType pivot_col ;   /* current pivot column */
-  IndexType *cp ;     /* a column pointer */
-  IndexType *rp ;     /* a row pointer */
-  IndexType pivot_row ;   /* current pivot row */
-  IndexType *new_cp ;   /* modified column pointer */
-  IndexType *new_rp ;   /* modified row pointer */
-  IndexType pivot_row_start ; /* pointer to start of pivot row */
-  IndexType pivot_row_degree ;  /* number of columns in pivot row */
-  IndexType pivot_row_length ;  /* number of supercolumns in pivot row */
-  IndexType pivot_col_score ; /* score of pivot column */
-  IndexType needed_memory ;   /* free space needed for pivot row */
-  IndexType *cp_end ;   /* pointer to the end of a column */
-  IndexType *rp_end ;   /* pointer to the end of a row */
-  IndexType row ;     /* a row index */
-  IndexType col ;     /* a column index */
-  IndexType max_score ;   /* maximum possible score */
-  IndexType cur_score ;   /* score of current column */
-  unsigned int hash ;   /* hash value for supernode detection */
-  IndexType head_column ;   /* head of hash bucket */
-  IndexType first_col ;   /* first column in hash bucket */
-  IndexType tag_mark ;    /* marker value for mark array */
-  IndexType row_mark ;    /* Row [row].shared2.mark */
-  IndexType set_difference ;  /* set difference size of row with pivot row */
-  IndexType min_score ;   /* smallest column score */
-  IndexType col_thickness ;   /* "thickness" (no. of columns in a supercol) */
-  IndexType max_mark ;    /* maximum value of tag_mark */
-  IndexType pivot_col_thickness ; /* number of columns represented by pivot col */
-  IndexType prev_col ;    /* Used by Dlist operations. */
-  IndexType next_col ;    /* Used by Dlist operations. */
-  IndexType ngarbage ;    /* number of garbage collections performed */
-
-
-  /* === Initialization and clear mark ==================================== */
-
-  max_mark = INT_MAX - n_col ;  /* INT_MAX defined in <limits.h> */
-  tag_mark = Colamd::clear_mark (n_row, Row) ;
-  min_score = 0 ;
-  ngarbage = 0 ;
-  COLAMD_DEBUG1 (("colamd: Ordering, n_col2=%d\n", n_col2)) ;
-
-  /* === Order the columns ================================================ */
-
-  for (k = 0 ; k < n_col2 ; /* 'k' is incremented below */)
-  {
-
-    /* === Select pivot column, and order it ============================ */
-
-    /* make sure degree list isn't empty */
-    COLAMD_ASSERT (min_score >= 0) ;
-    COLAMD_ASSERT (min_score <= n_col) ;
-    COLAMD_ASSERT (head [min_score] >= Empty) ;
-
-    /* get pivot column from head of minimum degree list */
-    while (min_score < n_col && head [min_score] == Empty)
-    {
-      min_score++ ;
-    }
-    pivot_col = head [min_score] ;
-    COLAMD_ASSERT (pivot_col >= 0 && pivot_col <= n_col) ;
-    next_col = Col [pivot_col].shared4.degree_next ;
-    head [min_score] = next_col ;
-    if (next_col != Empty)
-    {
-      Col [next_col].shared3.prev = Empty ;
-    }
-
-    COLAMD_ASSERT (Col[pivot_col].is_alive()) ;
-    COLAMD_DEBUG3 (("Pivot col: %d\n", pivot_col)) ;
-
-    /* remember score for defrag check */
-    pivot_col_score = Col [pivot_col].shared2.score ;
-
-    /* the pivot column is the kth column in the pivot order */
-    Col [pivot_col].shared2.order = k ;
-
-    /* increment order count by column thickness */
-    pivot_col_thickness = Col [pivot_col].shared1.thickness ;
-    k += pivot_col_thickness ;
-    COLAMD_ASSERT (pivot_col_thickness > 0) ;
-
-    /* === Garbage_collection, if necessary ============================= */
-
-    needed_memory = numext::mini(pivot_col_score, n_col - k) ;
-    if (pfree + needed_memory >= Alen)
-    {
-      pfree = Colamd::garbage_collection (n_row, n_col, Row, Col, A, &A [pfree]) ;
-      ngarbage++ ;
-      /* after garbage collection we will have enough */
-      COLAMD_ASSERT (pfree + needed_memory < Alen) ;
-      /* garbage collection has wiped out the Row[].shared2.mark array */
-      tag_mark = Colamd::clear_mark (n_row, Row) ;
-
-    }
-
-    /* === Compute pivot row pattern ==================================== */
-
-    /* get starting location for this new merged row */
-    pivot_row_start = pfree ;
-
-    /* initialize new row counts to zero */
-    pivot_row_degree = 0 ;
-
-    /* tag pivot column as having been visited so it isn't included */
-    /* in merged pivot row */
-    Col [pivot_col].shared1.thickness = -pivot_col_thickness ;
-
-    /* pivot row is the union of all rows in the pivot column pattern */
-    cp = &A [Col [pivot_col].start] ;
-    cp_end = cp + Col [pivot_col].length ;
-    while (cp < cp_end)
-    {
-      /* get a row */
-      row = *cp++ ;
-      COLAMD_DEBUG4 (("Pivot col pattern %d %d\n", Row[row].is_alive(), row)) ;
-      /* skip if row is dead */
-      if (Row[row].is_dead())
-      {
-	continue ;
-      }
-      rp = &A [Row [row].start] ;
-      rp_end = rp + Row [row].length ;
-      while (rp < rp_end)
-      {
-	/* get a column */
-	col = *rp++ ;
-	/* add the column, if alive and untagged */
-	col_thickness = Col [col].shared1.thickness ;
-	if (col_thickness > 0 && Col[col].is_alive())
-	{
-	  /* tag column in pivot row */
-	  Col [col].shared1.thickness = -col_thickness ;
-	  COLAMD_ASSERT (pfree < Alen) ;
-	  /* place column in pivot row */
-	  A [pfree++] = col ;
-	  pivot_row_degree += col_thickness ;
-	}
-      }
-    }
-
-    /* clear tag on pivot column */
-    Col [pivot_col].shared1.thickness = pivot_col_thickness ;
-    max_deg = numext::maxi(max_deg, pivot_row_degree) ;
-
-
-    /* === Kill all rows used to construct pivot row ==================== */
-
-    /* also kill pivot row, temporarily */
-    cp = &A [Col [pivot_col].start] ;
-    cp_end = cp + Col [pivot_col].length ;
-    while (cp < cp_end)
-    {
-      /* may be killing an already dead row */
-      row = *cp++ ;
-      COLAMD_DEBUG3 (("Kill row in pivot col: %d\n", row)) ;
-      Row[row].kill() ;
-    }
-
-    /* === Select a row index to use as the new pivot row =============== */
-
-    pivot_row_length = pfree - pivot_row_start ;
-    if (pivot_row_length > 0)
-    {
-      /* pick the "pivot" row arbitrarily (first row in col) */
-      pivot_row = A [Col [pivot_col].start] ;
-      COLAMD_DEBUG3 (("Pivotal row is %d\n", pivot_row)) ;
-    }
-    else
-    {
-      /* there is no pivot row, since it is of zero length */
-      pivot_row = Empty ;
-      COLAMD_ASSERT (pivot_row_length == 0) ;
-    }
-    COLAMD_ASSERT (Col [pivot_col].length > 0 || pivot_row_length == 0) ;
-
-    /* === Approximate degree computation =============================== */
-
-    /* Here begins the computation of the approximate degree.  The column */
-    /* score is the sum of the pivot row "length", plus the size of the */
-    /* set differences of each row in the column minus the pattern of the */
-    /* pivot row itself.  The column ("thickness") itself is also */
-    /* excluded from the column score (we thus use an approximate */
-    /* external degree). */
-
-    /* The time taken by the following code (compute set differences, and */
-    /* add them up) is proportional to the size of the data structure */
-    /* being scanned - that is, the sum of the sizes of each column in */
-    /* the pivot row.  Thus, the amortized time to compute a column score */
-    /* is proportional to the size of that column (where size, in this */
-    /* context, is the column "length", or the number of row indices */
-    /* in that column).  The number of row indices in a column is */
-    /* monotonically non-decreasing, from the length of the original */
-    /* column on input to colamd. */
-
-    /* === Compute set differences ====================================== */
-
-    COLAMD_DEBUG3 (("** Computing set differences phase. **\n")) ;
-
-    /* pivot row is currently dead - it will be revived later. */
-
-    COLAMD_DEBUG3 (("Pivot row: ")) ;
-    /* for each column in pivot row */
-    rp = &A [pivot_row_start] ;
-    rp_end = rp + pivot_row_length ;
-    while (rp < rp_end)
-    {
-      col = *rp++ ;
-      COLAMD_ASSERT (Col[col].is_alive() && col != pivot_col) ;
-      COLAMD_DEBUG3 (("Col: %d\n", col)) ;
-
-      /* clear tags used to construct pivot row pattern */
-      col_thickness = -Col [col].shared1.thickness ;
-      COLAMD_ASSERT (col_thickness > 0) ;
-      Col [col].shared1.thickness = col_thickness ;
-
-      /* === Remove column from degree list =========================== */
-
-      cur_score = Col [col].shared2.score ;
-      prev_col = Col [col].shared3.prev ;
-      next_col = Col [col].shared4.degree_next ;
-      COLAMD_ASSERT (cur_score >= 0) ;
-      COLAMD_ASSERT (cur_score <= n_col) ;
-      COLAMD_ASSERT (cur_score >= Empty) ;
-      if (prev_col == Empty)
-      {
-	head [cur_score] = next_col ;
-      }
-      else
-      {
-	Col [prev_col].shared4.degree_next = next_col ;
-      }
-      if (next_col != Empty)
-      {
-	Col [next_col].shared3.prev = prev_col ;
-      }
-
-      /* === Scan the column ========================================== */
-
-      cp = &A [Col [col].start] ;
-      cp_end = cp + Col [col].length ;
-      while (cp < cp_end)
-      {
-	/* get a row */
-	row = *cp++ ;
-	/* skip if dead */
-	if (Row[row].is_dead())
-	{
-	  continue ;
-	}
-  row_mark = Row [row].shared2.mark ;
-	COLAMD_ASSERT (row != pivot_row) ;
-	set_difference = row_mark - tag_mark ;
-	/* check if the row has been seen yet */
-	if (set_difference < 0)
-	{
-	  COLAMD_ASSERT (Row [row].shared1.degree <= max_deg) ;
-	  set_difference = Row [row].shared1.degree ;
-	}
-	/* subtract column thickness from this row's set difference */
-	set_difference -= col_thickness ;
-	COLAMD_ASSERT (set_difference >= 0) ;
-	/* absorb this row if the set difference becomes zero */
-	if (set_difference == 0)
-	{
-	  COLAMD_DEBUG3 (("aggressive absorption. Row: %d\n", row)) ;
-	  Row[row].kill() ;
-	}
-	else
-	{
-	  /* save the new mark */
-	  Row [row].shared2.mark = set_difference + tag_mark ;
-	}
-      }
-    }
-
-
-    /* === Add up set differences for each column ======================= */
-
-    COLAMD_DEBUG3 (("** Adding set differences phase. **\n")) ;
-
-    /* for each column in pivot row */
-    rp = &A [pivot_row_start] ;
-    rp_end = rp + pivot_row_length ;
-    while (rp < rp_end)
-    {
-      /* get a column */
-      col = *rp++ ;
-      COLAMD_ASSERT (Col[col].is_alive() && col != pivot_col) ;
-      hash = 0 ;
-      cur_score = 0 ;
-      cp = &A [Col [col].start] ;
-      /* compact the column */
-      new_cp = cp ;
-      cp_end = cp + Col [col].length ;
-
-      COLAMD_DEBUG4 (("Adding set diffs for Col: %d.\n", col)) ;
-
-      while (cp < cp_end)
-      {
-	/* get a row */
-	row = *cp++ ;
-	COLAMD_ASSERT(row >= 0 && row < n_row) ;
-	/* skip if dead */
-	if (Row [row].is_dead())
-	{
-	  continue ;
-	}
-  row_mark = Row [row].shared2.mark ;
-	COLAMD_ASSERT (row_mark > tag_mark) ;
-	/* compact the column */
-	*new_cp++ = row ;
-	/* compute hash function */
-	hash += row ;
-	/* add set difference */
-	cur_score += row_mark - tag_mark ;
-	/* integer overflow... */
-	cur_score = numext::mini(cur_score, n_col) ;
-      }
-
-      /* recompute the column's length */
-      Col [col].length = (IndexType) (new_cp - &A [Col [col].start]) ;
-
-      /* === Further mass elimination ================================= */
-
-      if (Col [col].length == 0)
-      {
-	COLAMD_DEBUG4 (("further mass elimination. Col: %d\n", col)) ;
-	/* nothing left but the pivot row in this column */
-	Col[col].kill_principal() ;
-	pivot_row_degree -= Col [col].shared1.thickness ;
-	COLAMD_ASSERT (pivot_row_degree >= 0) ;
-	/* order it */
-	Col [col].shared2.order = k ;
-	/* increment order count by column thickness */
-	k += Col [col].shared1.thickness ;
-      }
-      else
-      {
-	/* === Prepare for supercolumn detection ==================== */
-
-	COLAMD_DEBUG4 (("Preparing supercol detection for Col: %d.\n", col)) ;
-
-	/* save score so far */
-	Col [col].shared2.score = cur_score ;
-
-	/* add column to hash table, for supercolumn detection */
-	hash %= n_col + 1 ;
-
-	COLAMD_DEBUG4 ((" Hash = %d, n_col = %d.\n", hash, n_col)) ;
-	COLAMD_ASSERT (hash <= n_col) ;
-
-	head_column = head [hash] ;
-	if (head_column > Empty)
-	{
-	  /* degree list "hash" is non-empty, use prev (shared3) of */
-	  /* first column in degree list as head of hash bucket */
-	  first_col = Col [head_column].shared3.headhash ;
-	  Col [head_column].shared3.headhash = col ;
-	}
-	else
-	{
-	  /* degree list "hash" is empty, use head as hash bucket */
-	  first_col = - (head_column + 2) ;
-	  head [hash] = - (col + 2) ;
-	}
-	Col [col].shared4.hash_next = first_col ;
-
-	/* save hash function in Col [col].shared3.hash */
-	Col [col].shared3.hash = (IndexType) hash ;
-	COLAMD_ASSERT (Col[col].is_alive()) ;
-      }
-    }
-
-    /* The approximate external column degree is now computed.  */
-
-    /* === Supercolumn detection ======================================== */
-
-    COLAMD_DEBUG3 (("** Supercolumn detection phase. **\n")) ;
-
-    Colamd::detect_super_cols (Col, A, head, pivot_row_start, pivot_row_length) ;
-
-    /* === Kill the pivotal column ====================================== */
-
-    Col[pivot_col].kill_principal() ;
-
-    /* === Clear mark =================================================== */
-
-    tag_mark += (max_deg + 1) ;
-    if (tag_mark >= max_mark)
-    {
-      COLAMD_DEBUG2 (("clearing tag_mark\n")) ;
-      tag_mark = Colamd::clear_mark (n_row, Row) ;
-    }
-
-    /* === Finalize the new pivot row, and column scores ================ */
-
-    COLAMD_DEBUG3 (("** Finalize scores phase. **\n")) ;
-
-    /* for each column in pivot row */
-    rp = &A [pivot_row_start] ;
-    /* compact the pivot row */
-    new_rp = rp ;
-    rp_end = rp + pivot_row_length ;
-    while (rp < rp_end)
-    {
-      col = *rp++ ;
-      /* skip dead columns */
-      if (Col[col].is_dead())
-      {
-	continue ;
-      }
-      *new_rp++ = col ;
-      /* add new pivot row to column */
-      A [Col [col].start + (Col [col].length++)] = pivot_row ;
-
-      /* retrieve score so far and add on pivot row's degree. */
-      /* (we wait until here for this in case the pivot */
-      /* row's degree was reduced due to mass elimination). */
-      cur_score = Col [col].shared2.score + pivot_row_degree ;
-
-      /* calculate the max possible score as the number of */
-      /* external columns minus the 'k' value minus the */
-      /* columns thickness */
-      max_score = n_col - k - Col [col].shared1.thickness ;
-
-      /* make the score the external degree of the union-of-rows */
-      cur_score -= Col [col].shared1.thickness ;
-
-      /* make sure score is less or equal than the max score */
-      cur_score = numext::mini(cur_score, max_score) ;
-      COLAMD_ASSERT (cur_score >= 0) ;
-
-      /* store updated score */
-      Col [col].shared2.score = cur_score ;
-
-      /* === Place column back in degree list ========================= */
-
-      COLAMD_ASSERT (min_score >= 0) ;
-      COLAMD_ASSERT (min_score <= n_col) ;
-      COLAMD_ASSERT (cur_score >= 0) ;
-      COLAMD_ASSERT (cur_score <= n_col) ;
-      COLAMD_ASSERT (head [cur_score] >= Empty) ;
-      next_col = head [cur_score] ;
-      Col [col].shared4.degree_next = next_col ;
-      Col [col].shared3.prev = Empty ;
-      if (next_col != Empty)
-      {
-	Col [next_col].shared3.prev = col ;
-      }
-      head [cur_score] = col ;
-
-      /* see if this score is less than current min */
-      min_score = numext::mini(min_score, cur_score) ;
-
-    }
-
-    /* === Resurrect the new pivot row ================================== */
-
-    if (pivot_row_degree > 0)
-    {
-      /* update pivot row length to reflect any cols that were killed */
-      /* during super-col detection and mass elimination */
-      Row [pivot_row].start  = pivot_row_start ;
-      Row [pivot_row].length = (IndexType) (new_rp - &A[pivot_row_start]) ;
-      Row [pivot_row].shared1.degree = pivot_row_degree ;
-      Row [pivot_row].shared2.mark = 0 ;
-      /* pivot row is no longer dead */
-    }
-  }
-
-  /* === All principal columns have now been ordered ====================== */
-
-  return (ngarbage) ;
-}
-
-
-/* ========================================================================== */
-/* === order_children ======================================================= */
-/* ========================================================================== */
-
-/*
-  The find_ordering routine has ordered all of the principal columns (the
-  representatives of the supercolumns).  The non-principal columns have not
-  yet been ordered.  This routine orders those columns by walking up the
-  parent tree (a column is a child of the column which absorbed it).  The
-  final permutation vector is then placed in p [0 ... n_col-1], with p [0]
-  being the first column, and p [n_col-1] being the last.  It doesn't look
-  like it at first glance, but be assured that this routine takes time linear
-  in the number of columns.  Although not immediately obvious, the time
-  taken by this routine is O (n_col), that is, linear in the number of
-  columns.  Not user-callable.
-*/
-template <typename IndexType>
-static inline  void order_children
-(
-  /* === Parameters ======================================================= */
-
-  IndexType n_col,      /* number of columns of A */
-  ColStructure<IndexType> Col [],    /* of size n_col+1 */
-  IndexType p []      /* p [0 ... n_col-1] is the column permutation*/
-  )
-{
-  /* === Local variables ================================================== */
-
-  IndexType i ;     /* loop counter for all columns */
-  IndexType c ;     /* column index */
-  IndexType parent ;    /* index of column's parent */
-  IndexType order ;     /* column's order */
-
-  /* === Order each non-principal column ================================== */
-
-  for (i = 0 ; i < n_col ; i++)
-  {
-    /* find an un-ordered non-principal column */
-    COLAMD_ASSERT (col_is_dead(Col, i)) ;
-    if (!Col[i].is_dead_principal() && Col [i].shared2.order == Empty)
-    {
-      parent = i ;
-      /* once found, find its principal parent */
-      do
-      {
-	parent = Col [parent].shared1.parent ;
-      } while (!Col[parent].is_dead_principal()) ;
-
-      /* now, order all un-ordered non-principal columns along path */
-      /* to this parent.  collapse tree at the same time */
-      c = i ;
-      /* get order of parent */
-      order = Col [parent].shared2.order ;
-
-      do
-      {
-	COLAMD_ASSERT (Col [c].shared2.order == Empty) ;
-
-	/* order this column */
-	Col [c].shared2.order = order++ ;
-	/* collaps tree */
-	Col [c].shared1.parent = parent ;
-
-	/* get immediate parent of this column */
-	c = Col [c].shared1.parent ;
-
-	/* continue until we hit an ordered column.  There are */
-	/* guaranteed not to be anymore unordered columns */
-	/* above an ordered column */
-      } while (Col [c].shared2.order == Empty) ;
-
-      /* re-order the super_col parent to largest order for this group */
-      Col [parent].shared2.order = order ;
-    }
-  }
-
-  /* === Generate the permutation ========================================= */
-
-  for (c = 0 ; c < n_col ; c++)
-  {
-    p [Col [c].shared2.order] = c ;
-  }
-}
-
-
-/* ========================================================================== */
-/* === detect_super_cols ==================================================== */
-/* ========================================================================== */
-
-/*
-  Detects supercolumns by finding matches between columns in the hash buckets.
-  Check amongst columns in the set A [row_start ... row_start + row_length-1].
-  The columns under consideration are currently *not* in the degree lists,
-  and have already been placed in the hash buckets.
-
-  The hash bucket for columns whose hash function is equal to h is stored
-  as follows:
-
-  if head [h] is >= 0, then head [h] contains a degree list, so:
-
-  head [h] is the first column in degree bucket h.
-  Col [head [h]].headhash gives the first column in hash bucket h.
-
-  otherwise, the degree list is empty, and:
-
-  -(head [h] + 2) is the first column in hash bucket h.
-
-  For a column c in a hash bucket, Col [c].shared3.prev is NOT a "previous
-  column" pointer.  Col [c].shared3.hash is used instead as the hash number
-  for that column.  The value of Col [c].shared4.hash_next is the next column
-  in the same hash bucket.
-
-  Assuming no, or "few" hash collisions, the time taken by this routine is
-  linear in the sum of the sizes (lengths) of each column whose score has
-  just been computed in the approximate degree computation.
-  Not user-callable.
-*/
-template <typename IndexType>
-static void detect_super_cols
-(
-  /* === Parameters ======================================================= */
-
-  ColStructure<IndexType> Col [],    /* of size n_col+1 */
-  IndexType A [],     /* row indices of A */
-  IndexType head [],    /* head of degree lists and hash buckets */
-  IndexType row_start,    /* pointer to set of columns to check */
-  IndexType row_length    /* number of columns to check */
-)
-{
-  /* === Local variables ================================================== */
-
-  IndexType hash ;      /* hash value for a column */
-  IndexType *rp ;     /* pointer to a row */
-  IndexType c ;     /* a column index */
-  IndexType super_c ;   /* column index of the column to absorb into */
-  IndexType *cp1 ;      /* column pointer for column super_c */
-  IndexType *cp2 ;      /* column pointer for column c */
-  IndexType length ;    /* length of column super_c */
-  IndexType prev_c ;    /* column preceding c in hash bucket */
-  IndexType i ;     /* loop counter */
-  IndexType *rp_end ;   /* pointer to the end of the row */
-  IndexType col ;     /* a column index in the row to check */
-  IndexType head_column ;   /* first column in hash bucket or degree list */
-  IndexType first_col ;   /* first column in hash bucket */
-
-  /* === Consider each column in the row ================================== */
-
-  rp = &A [row_start] ;
-  rp_end = rp + row_length ;
-  while (rp < rp_end)
-  {
-    col = *rp++ ;
-    if (Col[col].is_dead())
-    {
-      continue ;
-    }
-
-    /* get hash number for this column */
-    hash = Col [col].shared3.hash ;
-    COLAMD_ASSERT (hash <= n_col) ;
-
-    /* === Get the first column in this hash bucket ===================== */
-
-    head_column = head [hash] ;
-    if (head_column > Empty)
-    {
-      first_col = Col [head_column].shared3.headhash ;
-    }
-    else
-    {
-      first_col = - (head_column + 2) ;
-    }
-
-    /* === Consider each column in the hash bucket ====================== */
-
-    for (super_c = first_col ; super_c != Empty ;
-	 super_c = Col [super_c].shared4.hash_next)
-    {
-      COLAMD_ASSERT (Col [super_c].is_alive()) ;
-      COLAMD_ASSERT (Col [super_c].shared3.hash == hash) ;
-      length = Col [super_c].length ;
-
-      /* prev_c is the column preceding column c in the hash bucket */
-      prev_c = super_c ;
-
-      /* === Compare super_c with all columns after it ================ */
-
-      for (c = Col [super_c].shared4.hash_next ;
-	   c != Empty ; c = Col [c].shared4.hash_next)
-      {
-	COLAMD_ASSERT (c != super_c) ;
-	COLAMD_ASSERT (Col[c].is_alive()) ;
-	COLAMD_ASSERT (Col [c].shared3.hash == hash) ;
-
-	/* not identical if lengths or scores are different */
-	if (Col [c].length != length ||
-	    Col [c].shared2.score != Col [super_c].shared2.score)
-	{
-	  prev_c = c ;
-	  continue ;
-	}
-
-	/* compare the two columns */
-	cp1 = &A [Col [super_c].start] ;
-	cp2 = &A [Col [c].start] ;
-
-	for (i = 0 ; i < length ; i++)
-	{
-	  /* the columns are "clean" (no dead rows) */
-	  COLAMD_ASSERT ( cp1->is_alive() );
-	  COLAMD_ASSERT ( cp2->is_alive() );
-	  /* row indices will same order for both supercols, */
-	  /* no gather scatter necessary */
-	  if (*cp1++ != *cp2++)
-	  {
-	    break ;
-	  }
-	}
-
-	/* the two columns are different if the for-loop "broke" */
-	if (i != length)
-	{
-	  prev_c = c ;
-	  continue ;
-	}
-
-	/* === Got it!  two columns are identical =================== */
-
-	COLAMD_ASSERT (Col [c].shared2.score == Col [super_c].shared2.score) ;
-
-	Col [super_c].shared1.thickness += Col [c].shared1.thickness ;
-	Col [c].shared1.parent = super_c ;
-	Col[c].kill_non_principal() ;
-	/* order c later, in order_children() */
-	Col [c].shared2.order = Empty ;
-	/* remove c from hash bucket */
-	Col [prev_c].shared4.hash_next = Col [c].shared4.hash_next ;
-      }
-    }
-
-    /* === Empty this hash bucket ======================================= */
-
-    if (head_column > Empty)
-    {
-      /* corresponding degree list "hash" is not empty */
-      Col [head_column].shared3.headhash = Empty ;
-    }
-    else
-    {
-      /* corresponding degree list "hash" is empty */
-      head [hash] = Empty ;
-    }
-  }
-}
-
-
-/* ========================================================================== */
-/* === garbage_collection =================================================== */
-/* ========================================================================== */
-
-/*
-  Defragments and compacts columns and rows in the workspace A.  Used when
-  all available memory has been used while performing row merging.  Returns
-  the index of the first free position in A, after garbage collection.  The
-  time taken by this routine is linear is the size of the array A, which is
-  itself linear in the number of nonzeros in the input matrix.
-  Not user-callable.
-*/
-template <typename IndexType>
-static IndexType garbage_collection  /* returns the new value of pfree */
-  (
-    /* === Parameters ======================================================= */
-
-    IndexType n_row,      /* number of rows */
-    IndexType n_col,      /* number of columns */
-    RowStructure<IndexType> Row [],    /* row info */
-    ColStructure<IndexType> Col [],    /* column info */
-    IndexType A [],     /* A [0 ... Alen-1] holds the matrix */
-    IndexType *pfree      /* &A [0] ... pfree is in use */
-    )
-{
-  /* === Local variables ================================================== */
-
-  IndexType *psrc ;     /* source pointer */
-  IndexType *pdest ;    /* destination pointer */
-  IndexType j ;     /* counter */
-  IndexType r ;     /* a row index */
-  IndexType c ;     /* a column index */
-  IndexType length ;    /* length of a row or column */
-
-  /* === Defragment the columns =========================================== */
-
-  pdest = &A[0] ;
-  for (c = 0 ; c < n_col ; c++)
-  {
-    if (Col[c].is_alive())
-    {
-      psrc = &A [Col [c].start] ;
-
-      /* move and compact the column */
-      COLAMD_ASSERT (pdest <= psrc) ;
-      Col [c].start = (IndexType) (pdest - &A [0]) ;
-      length = Col [c].length ;
-      for (j = 0 ; j < length ; j++)
-      {
-	r = *psrc++ ;
-	if (Row[r].is_alive())
-	{
-	  *pdest++ = r ;
-	}
-      }
-      Col [c].length = (IndexType) (pdest - &A [Col [c].start]) ;
-    }
-  }
-
-  /* === Prepare to defragment the rows =================================== */
-
-  for (r = 0 ; r < n_row ; r++)
-  {
-    if (Row[r].is_alive())
-    {
-      if (Row [r].length == 0)
-      {
-        /* this row is of zero length.  cannot compact it, so kill it */
-        COLAMD_DEBUG3 (("Defrag row kill\n")) ;
-        Row[r].kill() ;
-      }
-      else
-      {
-        /* save first column index in Row [r].shared2.first_column */
-        psrc = &A [Row [r].start] ;
-        Row [r].shared2.first_column = *psrc ;
-        COLAMD_ASSERT (Row[r].is_alive()) ;
-        /* flag the start of the row with the one's complement of row */
-        *psrc = ones_complement(r) ;
-
-      }
-    }
-  }
-
-  /* === Defragment the rows ============================================== */
-
-  psrc = pdest ;
-  while (psrc < pfree)
-  {
-    /* find a negative number ... the start of a row */
-    if (*psrc++ < 0)
-    {
-      psrc-- ;
-      /* get the row index */
-      r = ones_complement(*psrc) ;
-      COLAMD_ASSERT (r >= 0 && r < n_row) ;
-      /* restore first column index */
-      *psrc = Row [r].shared2.first_column ;
-      COLAMD_ASSERT (Row[r].is_alive()) ;
-
-      /* move and compact the row */
-      COLAMD_ASSERT (pdest <= psrc) ;
-      Row [r].start = (IndexType) (pdest - &A [0]) ;
-      length = Row [r].length ;
-      for (j = 0 ; j < length ; j++)
-      {
-	c = *psrc++ ;
-	if (Col[c].is_alive())
-	{
-	  *pdest++ = c ;
-	}
-      }
-      Row [r].length = (IndexType) (pdest - &A [Row [r].start]) ;
-
-    }
-  }
-  /* ensure we found all the rows */
-  COLAMD_ASSERT (debug_rows == 0) ;
-
-  /* === Return the new value of pfree ==================================== */
-
-  return ((IndexType) (pdest - &A [0])) ;
-}
-
-
-/* ========================================================================== */
-/* === clear_mark =========================================================== */
-/* ========================================================================== */
-
-/*
-  Clears the Row [].shared2.mark array, and returns the new tag_mark.
-  Return value is the new tag_mark.  Not user-callable.
-*/
-template <typename IndexType>
-static inline  IndexType clear_mark  /* return the new value for tag_mark */
-  (
-      /* === Parameters ======================================================= */
-
-    IndexType n_row,    /* number of rows in A */
-    RowStructure<IndexType> Row [] /* Row [0 ... n_row-1].shared2.mark is set to zero */
-    )
-{
-  /* === Local variables ================================================== */
-
-  IndexType r ;
-
-  for (r = 0 ; r < n_row ; r++)
-  {
-    if (Row[r].is_alive())
-    {
-      Row [r].shared2.mark = 0 ;
-    }
-  }
-  return (1) ;
-}
-
-} // namespace Colamd
-
-} // namespace internal
-#endif