v2.3.0

AMD/Demo/amd_demo.out

@@ -1,7 +1,7 @@
-AMD version 2.0, date: May 5, 2006
+AMD version 2.0, date: Nov 29, 2006
 AMD demo, with the 24-by-24 Harwell/Boeing matrix, can_24:
 
-amd version 2.0, May 5, 2006:  approximate minimum degree ordering:
+amd version 2.0, Nov 29, 2006:  approximate minimum degree ordering:
     dense row parameter: 10
     (rows with more than max (10 * sqrt (n), 16) entries are
     considered "dense", and placed last in output permutation)

AMD/Demo/amd_demo2.out

@@ -1,7 +1,7 @@
 AMD demo, with a jumbled version of the 24-by-24
 Harwell/Boeing matrix, can_24:
 
-amd version 2.0, May 5, 2006:  approximate minimum degree ordering:
+amd version 2.0, Nov 29, 2006:  approximate minimum degree ordering:
     dense row parameter: 10
     (rows with more than max (10 * sqrt (n), 16) entries are
     considered "dense", and placed last in output permutation)

AMD/Demo/amd_l_demo.out

@@ -1,7 +1,7 @@
-AMD version 2.0, date: May 5, 2006
+AMD version 2.0, date: Nov 29, 2006
 AMD demo, with the 24-by-24 Harwell/Boeing matrix, can_24:
 
-amd version 2.0, May 5, 2006:  approximate minimum degree ordering:
+amd version 2.0, Nov 29, 2006:  approximate minimum degree ordering:
     dense row parameter: 10
     (rows with more than max (10 * sqrt (n), 16) entries are
     considered "dense", and placed last in output permutation)

AMD/Doc/AMD_UserGuide.tex

@@ -34,7 +34,7 @@
 This work was supported by the EPSRC under grant GR/R46441.
 }}
 
-\date{May 5, 2006}
+\date{Nov 29, 2006}
 \maketitle
 
 %------------------------------------------------------------------------------
@@ -182,8 +182,17 @@ \section{Availability}
 \section{Using AMD in MATLAB}
 %------------------------------------------------------------------------------
 
-To use AMD in MATLAB, you must first compile the AMD mexFunction.
-Just type {\tt make} in the Unix system shell, while in the {\tt AMD}
+The MATLAB function {\tt amd} is now a built-in function in MATLAB 7.3
+(R2006b).  Compiling the AMD mexFunction, here, causes a name conflict
+(it is MATLAB that is conflict with AMD, not the other way around ...).
+
+To avoid this issue, either use the built-in {\tt amd}, or use the
+{\tt amd2} function provided here.  {\tt amd}
+and {\tt amd2} differ in how the optional parameters are passed
+(the 2nd input parameter).
+
+To use AMD2 in MATLAB, you must first compile the AMD2 mexFunction.
+Just type {\tt make} in the Unix system shell, while in the {\tt AMD/MATLAB}
 directory.  You can also type {\tt amd\_make} in MATLAB, while in the
 {\tt AMD/MATLAB} directory.  Place the {\tt AMD/MATLAB} directory in your
 MATLAB path.  This can be done on any system with MATLAB, including Windows.
@@ -719,11 +728,12 @@ \section{Installation}
 you need to add the {\tt AMD/Lib/libamdf77.a} library.
 See {\tt AMD/Demo/Makefile} for an example.
 
-If all you want to use is the AMD mexFunction in MATLAB, you can skip
+If all you want to use is the AMD2 mexFunction in MATLAB, you can skip
 the use of the {\tt make} command entirely.  Simply type
 {\tt amd\_make} in MATLAB while in the {\tt AMD/MATLAB} directory.
 This works on any system with MATLAB, including Windows.
-Alternately, type {\tt make} in the {\tt AMD/MATLAB} directory.
+Alternately, type {\tt make} in the {\tt AMD/MATLAB} directory,
+or just use the built-in {\tt amd} in MATLAB 7.3 or later.
 
 If you are including AMD as a subset of a larger library and do not want
 to link the C standard I/O library, or if you simply do not need to use
@@ -1166,10 +1176,11 @@ \section{The AMD routines}
  * Versions 1.1 and earlier of AMD do not include a #define'd version number.
  */
 
-#define AMD_DATE "May 5, 2006"
+#define AMD_DATE "Nov 29, 2006"
 #define AMD_VERSION_CODE(main,sub) ((main) * 1000 + (sub))
 #define AMD_MAIN_VERSION 2
 #define AMD_SUB_VERSION 0
+#define AMD_SUBSUB_VERSION 3
 #define AMD_VERSION AMD_VERSION_CODE(AMD_MAIN_VERSION,AMD_SUB_VERSION)
 
 #ifdef __cplusplus
@@ -1180,6 +1191,7 @@ \section{The AMD routines}
 \end{verbatim}
 }
 
+
 %------------------------------------------------------------------------------
 \newpage
 % References

AMD/Doc/ChangeLog

@@ -1,3 +1,13 @@
+Nov 29, 2006, version 2.0.3
+
+    * changed MATLAB function name to amd2, so as not to conflict with
+	the now built-in version of AMD in MATLAB (which is the same thing
+	as the AMD here...).
+
+Sept 28, 2006, version 2.0.2
+
+    * #define SIZE_T_MAX not done if already defined (Mac OSX).
+
 Aug 31, 2006:
 
     * trivial change to comments in amd.m

AMD/Include/amd.h

@@ -398,10 +398,11 @@ void amd_l_info     (double Info [ ]) ;
  * Versions 1.1 and earlier of AMD do not include a #define'd version number.
  */
 
-#define AMD_DATE "May 5, 2006"
+#define AMD_DATE "Nov 29, 2006"
 #define AMD_VERSION_CODE(main,sub) ((main) * 1000 + (sub))
 #define AMD_MAIN_VERSION 2
 #define AMD_SUB_VERSION 0
+#define AMD_SUBSUB_VERSION 3
 #define AMD_VERSION AMD_VERSION_CODE(AMD_MAIN_VERSION,AMD_SUB_VERSION)
 
 #ifdef __cplusplus

AMD/Include/amd_internal.h

@@ -153,7 +153,9 @@
 #define NULL 0
 
 /* largest value of size_t */
+#ifndef SIZE_T_MAX
 #define SIZE_T_MAX ((size_t) (-1))
+#endif
 
 /* ------------------------------------------------------------------------- */
 /* integer type for AMD: int or UF_long */

AMD/MATLAB/Contents.m

@@ -1,11 +1,14 @@
 %Contents of the AMD sparse matrix ordering package:
 %
-% amd		    p = amd (A), the approximate minimum degree ordering of A
-% amd_demo	    a demo of amd, using the can_24 matrix
-% amd_make	    to compile amd for use in MATLAB
-% can_24.mat	    a sample sparse matrix from the Harwell/Boeing collection
+% amd2          p = amd2 (A), the approximate minimum degree ordering of A
+% amd_demo      a demo of amd2, using the can_24 matrix
+% amd_make      to compile amd2 for use in MATLAB
+% can_24.mat    a sample sparse matrix from the Harwell/Boeing collection
 %
-% See also:  amd, colamd, symamd, colmmd, symmmd, umfpack
+% See also:  amd, amd2, colamd, symamd, colmmd, symmmd, umfpack
+%
+% Note that amd2 and the built-in amd function in MATLAB 7.3 and later are one
+% and the same.
 %
 % --------------------------------------------------------------------------
 % AMD Version 2.0, Copyright (c) 2006 by Timothy A. Davis,

AMD/MATLAB/Makefile

@@ -2,17 +2,17 @@
 # Makefile for the AMD MATLAB mexFunction
 #------------------------------------------------------------------------------
 
-default: amd
+default: amd2
 
 include ../../UFconfig/UFconfig.mk
 
 AMD = ../Lib/libamd.a
 
 INC = -I../Include -I../../UFconfig
 
-amd: amd_mex.c
+amd2: amd_mex.c
 	( cd ../Source ; $(MAKE) )
-	$(MEX) $(INC) -output amd amd_mex.c $(AMD)
+	$(MEX) $(INC) -output amd2 amd_mex.c $(AMD)
 
 #------------------------------------------------------------------------------
 # Remove all but the files in the original distribution
@@ -24,4 +24,4 @@ clean:
 purge: distclean
 
 distclean: clean
-	- $(RM) amd.mex* amd.dll
+	- $(RM) amd2.mex* amd2.dll

AMD/MATLAB/amd.m → AMD/MATLAB/amd2.m

@@ -1,15 +1,18 @@
-function [p, Info] = amd (A, Control)
-%AMD Approximate minimum degree permutation.
-%    P = AMD (S) returns the approximate minimum degree permutation vector for
+function [p, Info] = amd2 (A, Control)					    %#ok
+%AMD2 Approximate minimum degree permutation.
+%    P = AMD2 (S) returns the approximate minimum degree permutation vector for
 %    the sparse matrix C = S+S'.  The Cholesky factorization of C (P,P), or
 %    S (P,P), tends to be sparser than that of C or S.  AMD tends to be faster
 %    than SYMMMD and SYMAMD, and tends to return better orderings than SYMMMD.
 %    S must be square. If S is full, amd(S) is equivalent to amd(sparse(S)).
 %
-%    Usage:  P = amd (S) ;                   % finds the ordering
-%            [P, Info] = amd (S, Control) ;  % optional parameters & statistics
-%            Control = amd ;                 % returns default parameters
-%            amd ;                           % prints default parameters.
+%    Note that the built-in AMD routine in MATLAB is identical to AMD2,
+%    except that AMD in MATLAB allows for a struct input to set the parameters.
+%
+%    Usage:  P = amd2 (S) ;                  % finds the ordering
+%            [P, Info] = amd2 (S, Control) ; % optional parameters & statistics
+%            Control = amd2 ;                % returns default parameters
+%            amd2 ;                          % prints default parameters.
 %
 %       Control (1); If S is n-by-n, then rows/columns with more than
 %           max (16, (Control (1))* sqrt(n)) entries in S+S' are considered
@@ -49,13 +52,17 @@
 %    of the approximate degree update used, and because "dense" rows/columns
 %    do not take part in the post-order.  It well-suited for a subsequent
 %    "chol", however.  If you require a precise elimination tree post-ordering,
-%    then do:
+%    then see the example below:
+%
+% Example:
 %
-%       P = amd (S) ;
+%       P = amd2 (S) ;
 %       C = spones (S) + spones (S') ;  % skip this if S already symmetric
 %       [ignore, Q] = etree (C (P,P)) ;
 %       P = P (Q) ;
 %
+% See also AMD, COLMMD, COLAMD, COLPERM, SYMAMD, SYMMMD, SYMRCM.
+
 % --------------------------------------------------------------------------
 % AMD Version 2.0, Copyright (c) 2006 by Timothy A. Davis,
 % Patrick R. Amestoy, and Iain S. Duff.  See ../README.txt for License.
@@ -65,8 +72,5 @@
 %
 %    Acknowledgements: This work was supported by the National Science
 %       Foundation, under grants ASC-9111263, DMS-9223088, and CCR-0203270.
-%
-%    See also COLMMD, COLAMD, COLPERM, SYMAMD, SYMMMD, SYMRCM.
 
-help amd
-error ('amd mexFunction not found!  Type "amd_make" in MATLAB to compile amd');
+error ('amd2 mexFunction not found') ;

AMD/MATLAB/amd_demo.m

@@ -10,13 +10,13 @@
 % web: http://www.cise.ufl.edu/research/sparse/amd
 % --------------------------------------------------------------------------
 %
-% See also: amd, amd_make
+% See also: amd, amd2, amd_make
 
 % This orders the same matrix as the ANSI C demo, amd_demo.c.  It includes an
 % additional analysis of the matrix via MATLAB's symbfact routine.
 
 % First, print the help information for AMD
-help amd
+help amd2
 
 % Get the Harwell/Boeing can_24 matrix.
 
@@ -38,10 +38,10 @@
 % order the matrix.  Note that the Info argument is optional.
 fprintf ('\nIf the next step fails, then you have\n') ;
 fprintf ('not yet compiled the AMD mexFunction.\n') ;
-[p, Info] = amd (A) ;
+[p, Info] = amd2 (A) ;
 
 % order again, but this time print some statistics
-[p, Info] = amd (A, [10 1 1]) ;
+[p, Info] = amd2 (A, [10 1 1]) ;
 
 fprintf ('Permutation vector:\n') ;
 fprintf (' %2d', p) ;

AMD/MATLAB/amd_make.m

@@ -8,8 +8,12 @@
 % web: http://www.cise.ufl.edu/research/sparse/amd
 % --------------------------------------------------------------------------
 
+if (~isempty (strfind (computer, '64')))
+    error ('64-bit version not yet supported') ;
+end
+
 i = sprintf ('-I..%sInclude -I..%s..%sUFconfig', filesep, filesep, filesep) ;
-cmd = sprintf ('mex -inline -O -output amd %s amd_mex.c', i) ;
+cmd = sprintf ('mex -inline -O -output amd2 %s amd_mex.c', i) ;
 files = {'amd_order', 'amd_dump', 'amd_postorder', 'amd_post_tree', ...
     'amd_aat', 'amd_2', 'amd_1', 'amd_defaults', 'amd_control', ...
     'amd_info', 'amd_valid', 'amd_global', 'amd_preprocess' } ;

AMD/README.txt

@@ -18,7 +18,9 @@ Quick start (for MATLAB users);
 
     To compile, test, and install the AMD mexFunction, cd to the
     AMD/MATLAB directory and type amd_make at the MATLAB prompt.
-    This works on any system supported by MATLAB.
+
+    NOTE: DO NOT ATTEMPT TO USE THIS CODE IN 64-BIT MATLAB (v7.3).
+    It is not yet ported to that version of MATLAB.
 
 -------------------------------------------------------------------------------
 
@@ -194,9 +196,9 @@ Files and directories in the AMD distribution:
     GNUmakefile			a nice Makefile, for GNU make
     Makefile			an ugly Unix Makefile (for older make's)
 
-    Contents.m			for "help amd" listing of toolbox contents
+    Contents.m			for "help amd2" listing of toolbox contents
 
-    amd.m			MATLAB help file for AMD
+    amd2.m			MATLAB help file for AMD
     amd_make.m			MATLAB m-file for compiling AMD mexFunction
 
     amd_mex.c			AMD mexFunction for MATLAB

CAMD/Doc/ChangeLog

@@ -1,3 +1,7 @@
+Sept 28, 2006, v2.1.2
+
+    * #define SIZE_T_MAX not done if already defined (Mac OSX).
+
 Aug 31, 2006: v2.1.1
 
     * trivial change to comments in camd.m

CAMD/Include/camd.h

@@ -405,10 +405,11 @@ void camd_l_info     (double Info [ ]) ;
  *	#endif
  */
 
-#define CAMD_DATE "June 27, 2006"
+#define CAMD_DATE "Sept 28, 2006"
 #define CAMD_VERSION_CODE(main,sub) ((main) * 1000 + (sub))
 #define CAMD_MAIN_VERSION 2
 #define CAMD_SUB_VERSION 1
+#define CAMD_SUBSUB_VERSION 2
 #define CAMD_VERSION CAMD_VERSION_CODE(CAMD_MAIN_VERSION,CAMD_SUB_VERSION)
 
 #ifdef __cplusplus

CAMD/Include/camd_internal.h

@@ -154,7 +154,9 @@
 #define NULL 0
 
 /* largest value of size_t */
+#ifndef SIZE_T_MAX
 #define SIZE_T_MAX ((size_t) (-1))
+#endif
 
 /* ------------------------------------------------------------------------- */
 /* integer type for CAMD: int or UF_long */

CAMD/MATLAB/camd_make.m

@@ -8,6 +8,10 @@
 % web: http://www.cise.ufl.edu/research/sparse/camd
 % --------------------------------------------------------------------------
 
+if (~isempty (strfind (computer, '64')))
+    error ('64-bit version not yet supported') ;
+end
+
 i = sprintf ('-I..%sInclude -I..%s..%sUFconfig', filesep, filesep, filesep) ;
 cmd = sprintf ('mex -inline -O -output camd %s camd_mex.c', i) ;
 files = {'camd_order', 'camd_dump', 'camd_postorder', ...

CAMD/README.txt

@@ -17,7 +17,9 @@ Quick start (for MATLAB users);
 
     To compile, test, and install the CAMD mexFunction, cd to the
     CAMD/MATLAB directory and type camd_make at the MATLAB prompt.
-    This works on any system supported by MATLAB.
+
+    NOTE: DO NOT ATTEMPT TO USE THIS CODE IN 64-BIT MATLAB (v7.3).
+    It is not yet ported to that version of MATLAB.
 
 -------------------------------------------------------------------------------
 

CCOLAMD/README.txt

@@ -31,6 +31,9 @@ Other "make" targets:
 			libccolamd.a
     make distclean	removes all files not in the distribution
 
+    NOTE: DO NOT ATTEMPT TO USE THIS CODE IN 64-BIT MATLAB (v7.3).
+    It is not yet ported to that version of MATLAB.
+
 To use ccolamd and csymamd within an application written in C, all you need are
 colamd.c and colamd.h, which are the C-callable ccolamd/csymamd codes.
 See ccolamd.c for more information on how to call ccolamd from a C program.

CHOLMOD/Check/cholmod_check.c

@@ -3,7 +3,7 @@
 /* ========================================================================== */
 
 /* -----------------------------------------------------------------------------
- * CHOLMOD/Check Module.  Version 1.2. Copyright (C) 2005-2006, Timothy A. Davis
+ * CHOLMOD/Check Module.  Version 1.3. Copyright (C) 2005-2006, Timothy A. Davis
  * The CHOLMOD/Check Module is licensed under Version 2.1 of the GNU
  * Lesser General Public License.  See lesser.txt for a text of the license.
  * CHOLMOD is also available under other licenses; contact authors for details.