v5.8.0

CHOLMOD/Demo/lperf.m

@@ -2,7 +2,7 @@
 
 clear
 rng ('default')
-index = UFget ;
+index = ssget ;
 f = find (index.posdef & (index.amd_lnz > 0)) ;
 f = setdiff (f, [1425 228 353 354]) ; % not really posdef
 [ignore i] = sort (index.amd_lnz (f)) ;
@@ -15,7 +15,7 @@
 
 for k = 1:nmat
     id = f (k) ;
-    Prob = UFget (id, index)
+    Prob = ssget (id, index)
     A = Prob.A ;
     n = size (A,1) ;
 

CHOLMOD/Doc/ChangeLog

@@ -1,3 +1,9 @@
+June 30, 2020: no change to version number
+
+    * minor update to MATLAB tests: no change to compiled library,
+        so version number remains 3.0.14.
+    * replaced UFget with ssget in MATLAB tests
+
 Feb 20, 2020: version 3.0.14
 
     * minor update to cholmod_check to print a matrix

CHOLMOD/MATLAB/README.txt

@@ -10,9 +10,9 @@ the MATLAB command line, while in the CHOLMOD/MATLAB directory.
 cholmod_demo is a short demo program for CHOLMOD.  Type "cholmod_demo" in
 your MATLAB command window to test your newly compiling CHOLMOD functions.
 Test/cholmod_test.m runs the test suite for the MATLAB interface to CHOLMOD.
-It requires the "UFget" interface to the UF sparse matrix collection, but
-provides a more extensive test for CHOLMOD.  To obtain a copy of UFget, see
-http://www.suitesparse.com .
+It requires the "ssget" interface to the SuiteSparse matrix collection, but
+provides a more extensive test for CHOLMOD.  To obtain a copy of ssget, see
+http://sparse.tamu.edu.
 
 ----------------------------------------
 Using AMD, CCOLAMD, and COLAMD in MATLAB

CHOLMOD/MATLAB/Test/GB_spones_mex.c

@@ -0,0 +1,57 @@
+//------------------------------------------------------------------------------
+// GB_spones_mex: like spones(A) in MATLAB but do not drop zeros on input
+//------------------------------------------------------------------------------
+
+// The MATLAB built-in function spones(A) has changed, of MATLAB R2019b.
+// It now drops zeros on input.  Prior versions converted them to 1 on output.
+// The tests here use the old behavior, so this function replaces spones(A)
+// with GB_spones_mex (A), which has the old behavior of spones.
+
+#include "mex.h"
+#include <string.h>
+
+void mexFunction
+(
+    int nargout,
+    mxArray *pargout [ ],
+    int nargin,
+    const mxArray *pargin [ ]
+)
+{
+
+    //--------------------------------------------------------------------------
+    // check inputs
+    //--------------------------------------------------------------------------
+
+    if (nargin != 1 || nargout > 1 || !mxIsSparse (pargin [0]))
+    {
+        mexErrMsgTxt ("usage: C = GB_spones_mex (A), A must be sparse") ;
+    }
+
+    //--------------------------------------------------------------------------
+    // get the input matrix
+    //--------------------------------------------------------------------------
+
+    mwSize m = mxGetM (pargin [0]) ;
+    mwSize n = mxGetN (pargin [0]) ;
+    mwIndex *Ap = mxGetJc (pargin [0]) ;
+    mwIndex *Ai = mxGetIr (pargin [0]) ;
+    mwSize nz = Ap [n] ;
+
+    //--------------------------------------------------------------------------
+    // create the output matrix
+    //--------------------------------------------------------------------------
+
+    pargout [0] = mxCreateSparse (m, n, nz+1, mxREAL) ;
+    mwIndex *Cp = mxGetJc (pargout [0]) ;
+    mwIndex *Ci = mxGetIr (pargout [0]) ;
+    double *Cx = mxGetDoubles (pargout [0]) ;
+
+    memcpy (Cp, Ap, (n+1) * sizeof (mwIndex)) ;
+    memcpy (Ci, Ai, nz    * sizeof (mwIndex)) ;
+    for (mwSize p = 0 ; p < nz ; p++)
+    {
+        Cx [p] = 1 ;
+    }
+}
+

CHOLMOD/MATLAB/Test/cholmod_test.m

@@ -4,7 +4,8 @@ function cholmod_test (nmat, do_diary)
 % Example:
 % cholmod_test(nmat,do_diary)
 %
-% The UFget interface to the UF sparse matrix collection is required.
+% The ssget interface to the SuiteSparse matrix collection is required.
+% See sparse.tamu.edu.
 %
 % nmat is optional.  If present, it is the # of matrices used in
 %   tests 0, 8, 10, 11, 12, and 12.  tests 14 and 15 use 2*nmat matrices.
@@ -50,7 +51,7 @@ function cholmod_test (nmat, do_diary)
 % This extensive test is not included:
 % test28: test nesdis
 
-% Copyright 2006-2007, Timothy A. Davis, http://www.suitesparse.com
+% Copyright 2006-2020, Timothy A. Davis, http://www.suitesparse.com
 
 if (nargin < 2)
     do_diary = 0 ;
@@ -66,6 +67,7 @@ function cholmod_test (nmat, do_diary)
 
 fprintf ('Running CHOLMOD tests.\n') ;
 help cholmod_test
+mex -O -R2018a GB_spones_mex.c
 
 test_path = pwd ;
 % addpath (test_path) ;

CHOLMOD/MATLAB/Test/dg.m

@@ -7,7 +7,7 @@ function dg(A)
 
 % Copyright 2007, Timothy A. Davis, http://www.suitesparse.com
 
-A = spones (A) ;
+A = GB_spones_mex (A) ;
 [p cp cm] = nesdis (A, 'row') ;
 
 % get the corresponding column ordering.  Order the columns

CHOLMOD/MATLAB/Test/ltest.m

@@ -7,7 +7,7 @@
 % Copyright 2013, Timothy A. Davis, http://www.suitesparse.com
 
 rng ('default')
-index = UFget ;
+index = ssget ;
 
 %{
 f = find (index.nrows == index.ncols & index.amd_lnz > 0) ;
@@ -23,7 +23,7 @@
 
 for k = 1:nmat
     id = f (k) ;
-    Prob = UFget (id, index)
+    Prob = ssget (id, index)
     A = spones (Prob.A) ;
     n = size (A,1) ;
     A = A+A' ;

CHOLMOD/MATLAB/Test/lxtest.m

@@ -7,7 +7,7 @@
 % Copyright 2013, Timothy A. Davis, http://www.suitesparse.com
 
 rng ('default')
-index = UFget ;
+index = ssget ;
 
 %{
 f = find (index.posdef & index.amd_lnz > 0) ;
@@ -23,13 +23,13 @@
 
 for k = 1:nmat
     id = f (k) ;
-    Prob = UFget (id, index)
+    Prob = ssget (id, index)
     A = Prob.A ;
     n = size (A,1) ;
     [LD gunk p] = ldlchol (A) ;
     C = A (p,p) ;
     [count h parent post Lpattern] = symbfact (C, 'sym', 'lower') ;
-    if (~isequal (Lpattern, spones (LD)))
+    if (~isequal (Lpattern, GB_spones_mex (LD)))
         error ('!') ;
     end
 
@@ -44,8 +44,8 @@
     end
 
     D2 = chol (D) ;
-    L2 = L*D2 + 1e-50 * spones (L) ;
-    if (~isequal (spones (L), spones (L2)))
+    L2 = L*D2 + 1e-50 * GB_spones_mex (L) ;
+    if (~isequal (GB_spones_mex (L), GB_spones_mex (L2)))
         error ('oops') ;
     end
     err = norm (L2*L2' - C, 1) / norm (C, 1) ;

CHOLMOD/MATLAB/Test/n2.m

@@ -5,15 +5,15 @@
 
 % Copyright 2007, Timothy A. Davis, http://www.suitesparse.com
 
-index = UFget ;
+index = ssget ;
 f = find ((index.amd_lnz > 0) & (index.nrows > 200)) ;
 [ignore i] = sort (index.amd_lnz (f)) ;
 f = f (i) ;
 nmat = length (f) ;
 
 for i = f
 
-    Prob = UFget (i, index) ;
+    Prob = ssget (i, index) ;
     disp (Prob) ;
     A = spones (Prob.A) ;
     [m n] = size (A) ;

CHOLMOD/MATLAB/Test/nn.m

@@ -6,7 +6,7 @@
 
 % Copyright 2007, Timothy A. Davis, http://www.suitesparse.com
 
-index = UFget ;
+index = ssget ;
 f = find (index.amd_lnz > 0) ;
 [ignore i] = sort (index.amd_lnz (f)) ;
 f = f (i) ;
@@ -25,7 +25,7 @@
 for k = 1:nmat
 
     i = f (k) ;
-    Prob = UFget (i,index) ;
+    Prob = ssget (i,index) ;
     A = Prob.A ;
     [m n] = size (A) ;
 

CHOLMOD/MATLAB/Test/test0.m

@@ -1,4 +1,4 @@
-function test0 (nmat)
+function test0 (nmat,f)
 %TEST0 test most CHOLMOD functions
 % Example:
 %   test0(nmat)
@@ -9,18 +9,20 @@ function test0 (nmat)
 fprintf ('=================================================================\n');
 fprintf ('test0: test most CHOLMOD functions\n') ;
 
-% This test requires UFget, the MATLAB interface to the UF sparse matrix
-% collection.  You can obtain UFget from http://www.suitesparse.com.
+% This test requires ssget, the MATLAB interface to the UF sparse matrix
+% collection.  You can obtain ssget from http://www.suitesparse.com.
 
 try
-    index = UFget ;
+    index = ssget ;
 catch
     error ('Test aborted.  UF sparse matrix collection not available.\n') ;
 end
 
-f = find (index.posdef) ;
-[ignore i] = sort (index.nrows (f)) ;
-f = f (i) ;
+if (nargin < 2)
+    f = find (index.posdef) ;
+    [ignore i] = sort (index.nrows (f)) ;
+    f = f (i) ;
+end
 
 rand ('state', 0) ;
 randn ('state', 0) ;
@@ -60,7 +62,7 @@ function test0 (nmat)
 
     % try
 
-	Problem = UFget (i) ;
+	Problem = ssget (i) ;
 	A = Problem.A ; 
 	fprintf ('\n================== Problem: %d: %s  n: %d nnz: %d\n', ...
 	    i, Problem.name, size (A,1), nnz (A)) ;
@@ -250,9 +252,19 @@ function test0 (nmat)
 	if (nnz (LD5) ~= nnz (LD4))
 	    error ('!') ;
 	end
-	if (nnz (spones (LD5) - spones (LD4)) ~= 0)
-	    error ('!') ;
-	end
+
+        % revised June 30, 2020
+        if (nnz (GB_spones_mex (LD5) - GB_spones_mex (LD4)) ~= 0)
+            error ('!') ;
+        end
+
+%       if (nnz (spones (LD5) - spones (LD4)) ~= 0)
+%           % TODO: fails on ssget (878) because MATLAB changed spones(...).
+%           LD5 (262,246)
+%           LD4 (262,246)
+%           spones (LD5) - spones (LD4)
+%           error ('!') ;
+%       end
 
 	b = rand (n,2) ;
 	x = ldlsolve (LD4, b) ;

CHOLMOD/MATLAB/Test/test10.m

@@ -12,7 +12,7 @@ function test10 (nmat)
 rand ('state',0) ;
 randn ('state',0) ;
 
-index = UFget ;
+index = ssget ;
 f = find (index.posdef) ;
 [ignore i] = sort (index.nrows (f)) ;
 f = f (i) ;
@@ -71,7 +71,7 @@ function test10 (nmat)
 
 		if (~complexity)
 		    nn					%#ok
-		    Prob = UFget (nn)			%#ok
+		    Prob = ssget (nn)			%#ok
 		end
 		A = Prob.A ;
 		if (complexity)

CHOLMOD/MATLAB/Test/test11.m

@@ -13,7 +13,7 @@ function test11 (nmat)
 rand ('state',0) ;
 randn ('state',0) ;
 
-index = UFget ;
+index = ssget ;
 f = find (index.posdef) ;
 [ignore i] = sort (index.nrows (f)) ;
 f = f (i) ;
@@ -59,7 +59,7 @@ function test11 (nmat)
     % try
 
 	fprintf ('\n%3d: %s/%s\n', nn, index.Group {nn}, index.Name {nn}) ;
-	Prob = UFget (nn) ;
+	Prob = ssget (nn) ;
 	A = Prob.A ;
 	clear Prob
 	n = size (A,1) ;

CHOLMOD/MATLAB/Test/test11results.m

@@ -7,7 +7,7 @@
 % Copyright 2007, Timothy A. Davis, http://www.suitesparse.com
 
 load Results
-index = UFget ;
+index = ssget ;
 
 c = E1(1:kkk) < 1 & T1(1:kkk) > 0 ;
 m = E2(1:kkk) < 1 & T2(1:kkk) > 0 ;

CHOLMOD/MATLAB/Test/test12.m

@@ -9,7 +9,7 @@ function test12 (nmat)
 fprintf ('=================================================================\n');
 fprintf ('test12: test etree2 and compare with etree\n') ;
 
-index = UFget ;
+index = ssget ;
 
 % only test matrices with nrows = 109000 or less.  large ones nearly always
 % cause a MATLAB segfault.
@@ -60,7 +60,7 @@ function test12 (nmat)
 
     % try
 
-	Problem = UFget (i) ;
+	Problem = ssget (i) ;
 	A = spones (Problem.A) ;
 	[m n] = size (A) ;
 	fprintf ('\n%4d: %-20s nrow: %6d ncol: %6d nnz: %10d\n', ...

CHOLMOD/MATLAB/Test/test14.m

@@ -9,7 +9,7 @@ function test14 (nmat)
 fprintf ('=================================================================\n');
 fprintf ('test14: test metis, symbfact2, and etree2\n') ;
 
-index = UFget ;
+index = ssget ;
 
 [ignore f] = sort (max (index.nrows, index.ncols)) ;
 
@@ -39,7 +39,7 @@ function test14 (nmat)
 
     % try
 
-	Prob = UFget (i)						    %#ok
+	Prob = ssget (i)						    %#ok
 	A = Prob.A ;
 	[m n] = size (A) ;
 

CHOLMOD/MATLAB/Test/test15.m

@@ -8,7 +8,7 @@ function test15 (nmat)
 
 fprintf ('=================================================================\n');
 
-index = UFget ;
+index = ssget ;
 
 % only test matrices with nrows = 109000 or less.  large ones nearly always
 % cause a MATLAB segfault.
@@ -31,7 +31,7 @@ function test15 (nmat)
 
     % try
 
-	Problem = UFget (i) ;
+	Problem = ssget (i) ;
 	A = spones (Problem.A) ;
 	[m n] = size (A) ;
 	fprintf ('\n%4d: %-20s nrow: %6d ncol: %6d nnz: %10d\n', ...

CHOLMOD/MATLAB/Test/test16.m

@@ -12,7 +12,7 @@
 rand ('state',1) ;
 randn ('state',1) ;
 
-Prob = UFget (936)							    %#ok
+Prob = ssget (936)							    %#ok
 A = Prob.A ;
 % tic
 % [L,s,p] = lchol (A) ;