v2.4.0

AMD/Demo/amd_demo.out

@@ -1,7 +1,7 @@
-AMD version 2.0, date: Nov 29, 2006
+AMD version 2.0, date: Dec 12, 2006
 AMD demo, with the 24-by-24 Harwell/Boeing matrix, can_24:
 
-amd version 2.0, Nov 29, 2006:  approximate minimum degree ordering:
+amd version 2.0, Dec 12, 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, Nov 29, 2006:  approximate minimum degree ordering:
+amd version 2.0, Dec 12, 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: Nov 29, 2006
+AMD version 2.0, date: Dec 12, 2006
 AMD demo, with the 24-by-24 Harwell/Boeing matrix, can_24:
 
-amd version 2.0, Nov 29, 2006:  approximate minimum degree ordering:
+amd version 2.0, Dec 12, 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{Nov 29, 2006}
+\date{Dec 12, 2006}
 \maketitle
 
 %------------------------------------------------------------------------------
@@ -1176,11 +1176,11 @@ \section{The AMD routines}
  * Versions 1.1 and earlier of AMD do not include a #define'd version number.
  */
 
-#define AMD_DATE "Nov 29, 2006"
+#define AMD_DATE "Dec 12, 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_SUBSUB_VERSION 4
 #define AMD_VERSION AMD_VERSION_CODE(AMD_MAIN_VERSION,AMD_SUB_VERSION)
 
 #ifdef __cplusplus

AMD/Doc/ChangeLog

@@ -1,3 +1,7 @@
+Dec 12, 2006, version 2.0.4
+
+    * minor MATLAB code cleanup
+
 Nov 29, 2006, version 2.0.3
 
     * changed MATLAB function name to amd2, so as not to conflict with

AMD/Include/amd.h

@@ -398,11 +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 "Nov 29, 2006"
+#define AMD_DATE "Dec 12, 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_SUBSUB_VERSION 4
 #define AMD_VERSION AMD_VERSION_CODE(AMD_MAIN_VERSION,AMD_SUB_VERSION)
 
 #ifdef __cplusplus

AMD/MATLAB/Contents.m

@@ -1,15 +1,17 @@
 %Contents of the AMD sparse matrix ordering package:
 %
-% 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
+% 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
 %
 % 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.
 %
+% Example:
+%   p = amd2 (A) ;
+%
 % --------------------------------------------------------------------------
 % AMD Version 2.0, Copyright (c) 2006 by Timothy A. Davis,
 % Patrick R. Amestoy, and Iain S. Duff.  See ../README.txt for License.

AMD/MATLAB/amd2.m

@@ -1,5 +1,5 @@
 function [p, Info] = amd2 (A, Control)					    %#ok
-%AMD2 Approximate minimum degree permutation.
+%AMD2 p = amd2 (A), the approximate minimum degree ordering of A
 %    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
@@ -64,7 +64,7 @@
 % See also AMD, COLMMD, COLAMD, COLPERM, SYMAMD, SYMMMD, SYMRCM.
 
 % --------------------------------------------------------------------------
-% AMD Version 2.0, Copyright (c) 2006 by Timothy A. Davis,
+% Copyright 2006 by Timothy A. Davis,
 % Patrick R. Amestoy, and Iain S. Duff.  See ../README.txt for License.
 % email: davis at cise.ufl.edu    CISE Department, Univ. of Florida.
 % web: http://www.cise.ufl.edu/research/sparse/amd

AMD/MATLAB/amd_demo.m

@@ -1,10 +1,13 @@
 function amd_demo
-% AMD DEMO
+%AMD_DEMO a demo of amd2, using the can_24 matrix
 %
 % A demo of AMD for MATLAB.
 %
+% Example:
+%   amd_demo
+%
 % --------------------------------------------------------------------------
-% AMD Version 2.0, Copyright (c) 2006 by Timothy A. Davis,
+% Copyright 2006 by Timothy A. Davis,
 % Patrick R. Amestoy, and Iain S. Duff.  See ../README.txt for License.
 % email: davis at cise.ufl.edu    CISE Department, Univ. of Florida.
 % web: http://www.cise.ufl.edu/research/sparse/amd
@@ -38,7 +41,7 @@
 % 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] = amd2 (A) ;
+[p, Info] = amd2 (A) ;		%#ok
 
 % order again, but this time print some statistics
 [p, Info] = amd2 (A, [10 1 1]) ;
@@ -78,7 +81,7 @@
 fprintf ('number of nonzeros in L (including diagonal):      %d\n', lnz2) ;
 fprintf ('floating point operation count for chol (A (p,p)): %d\n\n', fl2) ;
 
-if (lnz2 ~= lnz | fl ~= fl2)
+if (lnz2 ~= lnz || fl ~= fl2)
     fprintf ('Note that the nonzero and flop counts from AMD are slight\n') ;
     fprintf ('upper bounds.  This is due to the approximate minimum degree\n');
     fprintf ('method used, in conjunction with "mass elimination".\n') ;

AMD/MATLAB/amd_demo.m.out

@@ -1,16 +1,18 @@
-
 amd_demo
- AMD Approximate minimum degree permutation.
-     P = AMD (S) returns the approximate minimum degree permutation vector for
+ AMD2 p = amd2 (A), the approximate minimum degree ordering of A
+     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
@@ -50,32 +52,22 @@ amd_demo
      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] = sparsfun ('symetree', C (P,P)) ;
+        [ignore, Q] = etree (C (P,P)) ;
         P = P (Q) ;
 
-  --------------------------------------------------------------------------
-  AMD Version 2.0, Copyright (c) 2006 by Timothy A. Davis,
-  Patrick R. Amestoy, and Iain S. Duff.  See ../README.txt for License.
-  email: davis at cise.ufl.edu    CISE Department, Univ. of Florida.
-  web: http://www.cise.ufl.edu/research/sparse/amd
-  --------------------------------------------------------------------------
-
-     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.
-
-
+  See also AMD, COLMMD, COLAMD, COLPERM, SYMAMD, SYMMMD, SYMRCM.
 
 
 If the next step fails, then you have
 not yet compiled the AMD mexFunction.
 
-amd version 2.0, May 5, 2006:  approximate minimum degree ordering:
+amd version 2.0, Dec 12, 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)
@@ -117,10 +109,51 @@ Permutation vector:
  23 21 11 24 13  6 17  9 15  5 16  8  2 10 14 18  1  3  4  7 12 19 22 20
 
 Analyze A(p,p) with MATLAB's symbfact routine:
-predicted nonzeros:    120
-predicted flops:       656
-predicted height:      16
-predicted front size:  7
+
+CHOLMOD version 1.1.0, May 5, 2006:  : status: OK
+  Architecture: Linux
+    sizeof(int):      4
+    sizeof(UF_long):  4
+    sizeof(void *):   4
+    sizeof(double):   8
+    sizeof(Int):      4 (CHOLMOD's basic integer)
+    sizeof(BLAS_INT): 4 (integer used in the BLAS)
+  Results from most recent analysis:
+    Cholesky flop count: 656
+    Nonzeros in L:       120
+  memory blocks in use:           3
+  memory in use (MB):           0.0
+  peak memory usage (MB):       0.0
+  maxrank:    update/downdate rank:   8
+  supernodal control: 1 40 (supernodal if flops/lnz >= 40)
+  nmethods=0: default strategy:  Try user permutation if given.  Try AMD.
+    Select best ordering tried.
+    method 0: user permutation (if given)
+    method 1: AMD (or COLAMD if factorizing AA')
+        prune_dense: for pruning dense nodes:   10
+        a dense node has degree >= max(16,(10)*sqrt(n))
+  OK
+
+CHOLMOD version 1.1.0, May 5, 2006:  : status: OK
+  Architecture: Linux
+    sizeof(int):      4
+    sizeof(UF_long):  4
+    sizeof(void *):   4
+    sizeof(double):   8
+    sizeof(Int):      4 (CHOLMOD's basic integer)
+    sizeof(BLAS_INT): 4 (integer used in the BLAS)
+  memory blocks in use:           0
+  memory in use (MB):           0.0
+  peak memory usage (MB):       0.0
+  maxrank:    update/downdate rank:   8
+  supernodal control: 1 40 (supernodal if flops/lnz >= 40)
+  nmethods=0: default strategy:  Try user permutation if given.  Try AMD.
+    Select best ordering tried.
+    method 0: user permutation (if given)
+    method 1: AMD (or COLAMD if factorizing AA')
+        prune_dense: for pruning dense nodes:   10
+        a dense node has degree >= max(16,(10)*sqrt(n))
+  OK
 number of nonzeros in L (including diagonal):      120
 floating point operation count for chol (A (p,p)): 656
 

AMD/MATLAB/amd_make.m

@@ -1,8 +1,13 @@
 function amd_make
-% AMD_MAKE:  compiles the AMD mexFunction for MATLAB
+%AMD_MAKE to compile amd2 for use in MATLAB
+%
+% Example:
+%   amd_make
+%
+% See also amd, amd2.
 %
 % --------------------------------------------------------------------------
-% AMD Version 2.0, Copyright (c) 2006 by Timothy A. Davis,
+% Copyright 2006 by Timothy A. Davis,
 % Patrick R. Amestoy, and Iain S. Duff.  See ../README.txt for License.
 % email: davis at cise.ufl.edu    CISE Department, Univ. of Florida.
 % web: http://www.cise.ufl.edu/research/sparse/amd

BTF/Doc/ChangeLog

@@ -1,3 +1,7 @@
+Dec 12, 2006: version 0.11
+
+    * minor MATLAB cleanup
+
 Apr 30, 2006:
 
     * minor editing of comments.  dmperm.c moved to MATLAB directory, since

BTF/Include/btf.h

@@ -206,10 +206,10 @@ int btf_order	    /* returns number of blocks found */
  *	#endif
  */
 
-#define BTF_DATE "May 5, 2006"
+#define BTF_DATE "Dec 12, 2006"
 #define BTF_VERSION_CODE(main,sub) ((main) * 1000 + (sub))
 #define BTF_MAIN_VERSION 0
-#define BTF_SUB_VERSION 9
+#define BTF_SUB_VERSION 11
 #define BTF_VERSION BTF_VERSION_CODE(BTF_MAIN_VERSION,BTF_SUB_VERSION)
 
 #ifdef __cplusplus

BTF/MATLAB/Contents.m

@@ -0,0 +1,21 @@
+% BTF ordering toolbox, including test codes
+%
+% Primary functions:
+%
+%   maxtrans   - finds a permutation of the columns of a sparse matrix
+%   strongcomp - Find a symmetric permutation to upper block triangular form.
+%
+% helper and test functions:
+%
+%   checkbtf   - ensure A(p,q) is in BTF form
+%   drawbtf    - plot the BTF form of a matrix
+%   td         - test script for BTF
+%   toobig     - list of matrices that are too big for dmperm
+%   trav       - exhaustive test script for BTF
+%   dp         - dmperm on a sparse matrix
+%
+% Example:
+%   Match = maxtrans (A)
+%   [p,q,r] = strongcomp (A)
+
+% Copyright 2006, Timothy A. Davis, University of Florida

BTF/MATLAB/checkbtf.m

@@ -1,9 +1,15 @@
 function checkbtf (A, p, q, r)
-% checkbtf (A, p, q, r)
+%CHECKBTF ensure A(p,q) is in BTF form
 %
 % A(p,q) is in BTF form, r the block boundaries
 %
-% [p,q,r] = dmperm (A) for example
+% Example:
+%   [p,q,r] = dmperm (A)
+%   checkbtf (A, p, q, r)
+%
+% See also drawbtf, maxtrans, strongcomp.
+
+% Copyright 2006, Timothy A. Davis, University of Florida
 
 [m n] = size (A) ;
 if (m ~= n)
@@ -21,24 +27,20 @@ function checkbtf (A, p, q, r)
 nblocks = length (r) - 1 ;
 
 if (r (1) ~= 1)
-    r
     error ('r(1) not one') ;
 end
 
 if (r (end) ~= n+1)
-    r
     error ('r(end) not n+1') ;
 end
 
-if (nblocks < 1 | nblocks > n)
-    nblocks
-    n
+if (nblocks < 1 || nblocks > n)
     error ('nblocks wrong') ;
 end
 
 nblocks = length (r) - 1 ;
 rdiff = r (2:(nblocks+1)) - r (1:nblocks) ;
-if (any (rdiff < 1) | any (rdiff > n))
+if (any (rdiff < 1) || any (rdiff > n))
     error ('r bad')
 end
 

BTF/MATLAB/dp.m

@@ -0,0 +1,9 @@
+function [p,q,cp,ssize] = dp (A)					    %#ok
+%DP dmperm on a sparse matrix
+% Example:
+%   [p,q,cp,ssize] = dp (A)
+% See also dmperm, strongcomp, maxtrans
+
+% Copyright 2006, Timothy A. Davis, University of Florida
+
+error ('dp mexFunction not found') ;

BTF/MATLAB/drawbtf.m

@@ -1,9 +1,15 @@
 function drawbtf (A, p, q, r)
-% drawbtf (A, p, q, r)
+%DRAWBTF plot the BTF form of a matrix
 %
 % A(p,q) is in BTF form, r the block boundaries
 %
-% [p,q,r] = dmperm (A) for example
+% Example:
+%   [p,q,r] = dmperm (A)
+%   drawbtf (A, p, q, r)
+%
+% See also checkbtf, maxtrans, strongcomp.
+
+% Copyright 2006, Timothy A. Davis, University of Florida
 
 nblocks = length (r) - 1 ;