v5.0.0

.gitignore

@@ -34,6 +34,7 @@ my_*.out
 *.swp
 .DS_Store
 .nfs*
+.pyc
 
 # ignore these specific programs in the Package/Demo directories
 AMD/Demo/amd_demo
@@ -191,6 +192,31 @@ RBio/Tcov/SuiteSparse_config.h
 RBio/Tcov/*.out
 RBio/Tcov/*.rb
 
+# GraphBLAS
+GraphBLAS/Demo/bfs_demo.out
+GraphBLAS/Demo/complex_demo.m
+GraphBLAS/Demo/mis_demo.out
+GraphBLAS/Demo/simple_demo.out
+GraphBLAS/Demo/wildtype_demo.out
+GraphBLAS/Demo/tri_demo.out
+GraphBLAS/Test/errlog.txt
+GraphBLAS/Test/log.txt
+GraphBLAS/Doc/GraphBLAS_UserGuide.out
+GraphBLAS/Tcov/cover_GB_2type_template.c
+GraphBLAS/Tcov/cover_GB_AxB_compare_template.c
+GraphBLAS/Tcov/cover_GB_AxB_factory.c
+GraphBLAS/Tcov/cover_GB_AxB_template.c
+GraphBLAS/Tcov/cover_GB_assoc_template.c
+GraphBLAS/Tcov/cover_GB_ops_template.c
+GraphBLAS/Tcov/cover_GB_qsort_template.c
+GraphBLAS/Tcov/cover_GB_semiring_template.c
+GraphBLAS/Tcov/cover_GB_subref_template.c
+GraphBLAS/Tcov/cover_gb.c
+GraphBLAS/Tcov/cover_gb_exp.c
+GraphBLAS/Tcov/errlog.txt
+GraphBLAS/Tcov/log.txt
+GraphBLAS/Tcov/gbstat.mat
+
 # Do not ignore this file
 !.gitignore
 

CHOLMOD/GPU/cholmod_gpu.c

@@ -23,6 +23,8 @@
 #include <cuda_runtime.h>
 #endif
 
+// #define HACK
+
 #define MINSIZE (64 * 1024 * 1024)
 
 /* ========================================================================== */
@@ -108,6 +110,10 @@ int CHOLMOD(gpu_memorysize)      /* returns 1 on error, 0 otherwise */
     {
         /* printf ("quick %lu\n", s) ; */
         *available_mem = s;
+#ifdef HACK
+        *total_mem     /= 2;
+        *available_mem /= 2;
+#endif
         return (0) ;  /* no error */
     }
 
@@ -138,6 +144,10 @@ int CHOLMOD(gpu_memorysize)      /* returns 1 on error, 0 otherwise */
 
 #endif
 
+#ifdef HACK
+        *total_mem     /= 2;
+        *available_mem /= 2;
+#endif
     return (0) ; /* no error */
 }
 

CHOLMOD/Supernodal/cholmod_super_symbolic.c

@@ -985,7 +985,8 @@ int CHOLMOD(super_symbolic)
     cholmod_common *Common
 )
 {
-    return (CHOLMOD(super_symbolic2) (TRUE, A, F, Parent, L, Common)) ;
+    return (CHOLMOD(super_symbolic2) (CHOLMOD_ANALYZE_FOR_CHOLESKY,
+        A, F, Parent, L, Common)) ;
 }
 #endif
 #endif

CSparse/Doc/ChangeLog

@@ -1,3 +1,8 @@
+Sept 12, 2017: version 3.2.0
+
+    * replaced UFget with ssget
+    * added comment to cs_lu.c
+
 May 4, 2016: version 3.1.9
 
     * minor changes to Makefile

CSparse/Include/cs.h

@@ -9,9 +9,9 @@
 #include "mex.h"
 #endif
 #define CS_VER 3                    /* CSparse Version */
-#define CS_SUBVER 1
-#define CS_SUBSUB 9
-#define CS_DATE "May 4, 2016"       /* CSparse release date */
+#define CS_SUBVER 2
+#define CS_SUBSUB 0
+#define CS_DATE "Sept 12, 2017"       /* CSparse release date */
 #define CS_COPYRIGHT "Copyright (c) Timothy A. Davis, 2006-2016"
 
 #ifdef MATLAB_MEX_FILE

CSparse/MATLAB/CSparse/cs_add.m

@@ -4,8 +4,8 @@
 %   where alpha and beta default to 1 if not present.
 %
 %   Example:
-%       Prob1 = UFget ('HB/ibm32') ;        A = Prob1.A ;
-%       Prob2 = UFget ('Hamrle/Hamrle1') ;  B = Prob2.A ;
+%       Prob1 = ssget ('HB/ibm32') ;        A = Prob1.A ;
+%       Prob2 = ssget ('Hamrle/Hamrle1') ;  B = Prob2.A ;
 %       C = cs_add (A,B) ;
 %       D = A+B ;                           % same as C
 %

CSparse/MATLAB/CSparse/cs_amd.m

@@ -12,7 +12,7 @@
 %                   where [m n] = size(A), except that colamd does not form A'*A
 %                   explicitly.
 %   Example:
-%       Prob = UFget ('HB/bcsstk01') ; A = Prob.A ;
+%       Prob = ssget ('HB/bcsstk01') ; A = Prob.A ;
 %       p = cs_amd (A) ;
 %       nnz (chol (A))
 %       nnz (chol (A (p,p)))

CSparse/MATLAB/CSparse/cs_chol.m

@@ -7,7 +7,7 @@
 %   cs_chol(A,0) keeps them.  They must be kept for cs_updown to work properly.
 %
 %   Example:
-%       Prob = UFget ('HB/bcsstk01') ; A = Prob.A ; [L,p] = cs_chol (A) ;
+%       Prob = ssget ('HB/bcsstk01') ; A = Prob.A ; [L,p] = cs_chol (A) ;
 %       cspy (A (p,p)) ;
 %       cspy (L) ;
 %

CSparse/MATLAB/CSparse/cs_cholsol.m

@@ -6,7 +6,7 @@
 %   with no dense rows, 3:amd(A'*A).  The default ordering option is 1.
 %
 %   Example:
-%       Prob = UFget ('HB/bcsstk01') ; A = Prob.A ; b = rand (size (A,1),1) ;
+%       Prob = ssget ('HB/bcsstk01') ; A = Prob.A ; b = rand (size (A,1),1) ;
 %       x = cs_cholsol (A,b) ; norm (A*x-b)
 %
 %   See also CS_CHOL, CS_AMD, CS_LUSOL, CS_QRSOL, MLDIVIDE.

CSparse/MATLAB/CSparse/cs_counts.m

@@ -8,7 +8,7 @@
 %   c = cs_counts(A,'sym'), same as cs_counts(A).
 %
 %   Example:
-%       Prob = UFget ('HB/bcsstk01') ; A = Prob.A ; c = cs_counts (A)
+%       Prob = ssget ('HB/bcsstk01') ; A = Prob.A ; c = cs_counts (A)
 %       full (sum (spones (chol (A)')))
 %
 %   See also SYMBFACT.

CSparse/MATLAB/CSparse/cs_dmperm.m

@@ -49,7 +49,7 @@
 %
 %
 %   Example:
-%       Prob = UFget ('HB/west0479') ; A = Prob.A ;  cspy (A) ;
+%       Prob = ssget ('HB/west0479') ; A = Prob.A ;  cspy (A) ;
 %       p = cs_dmperm (A) ;
 %       cspy (A (p,:)) ;
 %       [p q r s cc rr] = cs_dmperm (A) ;

CSparse/MATLAB/CSparse/cs_dmsol.m

@@ -4,7 +4,7 @@
 %   structurally rank deficient, and b is a full vector.
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; A = Prob.A ; b = rand (size (A,1),1) ;
+%       Prob = ssget ('HB/arc130') ; A = Prob.A ; b = rand (size (A,1),1) ;
 %       x = cs_dmsol (A,b) ; norm (A*x-b)
 %
 %   See also CS_QRSOL, CS_LUSOL, CS_DMPERM, SPRANK, RANK.

CSparse/MATLAB/CSparse/cs_dmspy.m

@@ -11,7 +11,7 @@
 %   used by cs_dmperm.
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; cs_dmspy (Prob.A) ;
+%       Prob = ssget ('HB/arc130') ; cs_dmspy (Prob.A) ;
 %
 %   See also CS_DMPERM, CS_DMSOL, DMPERM, SPRANK, SPY.
 

CSparse/MATLAB/CSparse/cs_droptol.m

@@ -4,7 +4,7 @@
 %   equal to tol.  Same as A = A .* (abs (A) >= tol).
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; A = Prob.A ;
+%       Prob = ssget ('HB/arc130') ; A = Prob.A ;
 %       cspy (abs (A) >= 1e-10) ;
 %       C = cs_droptol (A, 1e-10) ;
 %       cspy (C) ;

CSparse/MATLAB/CSparse/cs_esep.m

@@ -5,7 +5,7 @@
 %   set of entries in A(a,b).
 %
 %   Example:
-%       Prob = UFget ('HB/bcsstk01') ; A = Prob.A ;
+%       Prob = ssget ('HB/bcsstk01') ; A = Prob.A ;
 %       [a,b] = cs_esep (A) ;
 %       cspy (A (a,b)) ;
 %

CSparse/MATLAB/CSparse/cs_etree.m

@@ -8,7 +8,7 @@
 %   [parent,post] = cs_etree(...) also returns a postorder of the tree.
 %
 %   Example:
-%       Prob = UFget ('HB/bcsstk01') ; A = Prob.A ;
+%       Prob = ssget ('HB/bcsstk01') ; A = Prob.A ;
 %       parent = cs_etree (A) ; treeplot (parent) ;
 %
 %   See also ETREE, TREEPLOT.

CSparse/MATLAB/CSparse/cs_gaxpy.m

@@ -3,7 +3,7 @@
 %   z = cs_gaxpy(A,x,y) computes z = A*x+y where x and y are full vectors.
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; A = Prob.A ; [m n] = size (A) ;
+%       Prob = ssget ('HB/arc130') ; A = Prob.A ; [m n] = size (A) ;
 %       x = rand (n,1) ; y = rand (m,1) ;
 %       z = cs_gaxpy (A, x, y) ;
 %       

CSparse/MATLAB/CSparse/cs_lsolve.m

@@ -6,7 +6,7 @@
 %   is returned in topological order).
 %
 %   Example:
-%       Prob = UFget ('HB/bcsstk01') ; L = cs_chol (Prob.A) ; n = size (L,1) ;
+%       Prob = ssget ('HB/bcsstk01') ; L = cs_chol (Prob.A) ; n = size (L,1) ;
 %       b = rand (n,1) ; x = cs_lsolve (L,b) ; norm (L*x-b)
 %
 %   See also CS_LTSOLVE, CS_USOLVE, CS_UTSOLVE, MLDIVIDE.

CSparse/MATLAB/CSparse/cs_ltsolve.m

@@ -4,7 +4,7 @@
 %   zero-free diagonal.  b must be a full vector.
 %
 %   Example:
-%       Prob = UFget ('HB/bcsstk01') ; L = cs_chol (Prob.A) ; n = size (L,1) ;
+%       Prob = ssget ('HB/bcsstk01') ; L = cs_chol (Prob.A) ; n = size (L,1) ;
 %       b = rand (n,1) ; x = cs_ltsolve (L,b) ; norm (L'*x-b)
 %
 %   See also CS_LSOLVE, CS_USOLVE, CS_UTSOLVE, MLDIVIDE.

CSparse/MATLAB/CSparse/cs_lu.m

@@ -17,7 +17,7 @@
 %   pivoting; the diagonal is selected if it is >= tol * max(abs(A(:,k))).
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; A = Prob.A ; [L,U,p,q] = cs_lu (A) ;
+%       Prob = ssget ('HB/arc130') ; A = Prob.A ; [L,U,p,q] = cs_lu (A) ;
 %       cspy (A (p,q)) ; cspy (L+U) ;
 %       norm (L*U - A(p,q), 1)
 %

CSparse/MATLAB/CSparse/cs_lusol.m

@@ -12,7 +12,7 @@
 %   dense rows, 3: amd(A'*A).
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; A = Prob.A ; n = size(A,1) ;
+%       Prob = ssget ('HB/arc130') ; A = Prob.A ; n = size(A,1) ;
 %       b = rand (n,1) ; x = cs_lusol (A,b) ; norm (A*x-b)
 %
 %   See also CS_LU, CS_AMD, CS_CHOLSOL, CS_QRSOL, MLDIVIDE.

CSparse/MATLAB/CSparse/cs_multiply.m

@@ -3,8 +3,8 @@
 %   C = cs_multiply(A,B) computes C = A*B.
 %
 %   Example:
-%       Prob1 = UFget ('HB/ibm32') ;        A = Prob1.A ;
-%       Prob2 = UFget ('Hamrle/Hamrle1') ;  B = Prob2.A ;
+%       Prob1 = ssget ('HB/ibm32') ;        A = Prob1.A ;
+%       Prob2 = ssget ('Hamrle/Hamrle1') ;  B = Prob2.A ;
 %       C = cs_multiply (A,B) ;
 %       D = A*B ;                           % same as C
 %

CSparse/MATLAB/CSparse/cs_permute.m

@@ -3,7 +3,7 @@
 %   C = cs_permute(A,p,q) computes C = A(p,q)
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; A = Prob.A ; [m n] = size (A) ;
+%       Prob = ssget ('HB/arc130') ; A = Prob.A ; [m n] = size (A) ;
 %       p = randperm (m) ; q = randperm (n) ;
 %       C = cs_permute (A,p,q) ;    % C = A(p,q)
 %

CSparse/MATLAB/CSparse/cs_print.m

@@ -3,7 +3,7 @@ function cs_print (A,brief)                                                 %#ok
 %   cs_print(A) prints a sparse matrix. cs_print(A,1) prints just a few entries.
 %
 %   Example:
-%       Prob = UFget ('vanHeukelum/cage3') ; A = Prob.A
+%       Prob = ssget ('vanHeukelum/cage3') ; A = Prob.A
 %       cs_print (A) ;
 %
 %   See also: DISPLAY.

CSparse/MATLAB/CSparse/cs_qleft.m

@@ -5,7 +5,7 @@
 %   permutation p.  p can be [], which denotes the identity permutation.
 %
 %   Example:
-%       Prob = UFget ('HB/well1033') ; A = Prob.A ; [m n] = size (A) ;
+%       Prob = ssget ('HB/well1033') ; A = Prob.A ; [m n] = size (A) ;
 %       b = rand (m,1) ;
 %       [V,beta,p,R] = cs_qr (A) ; % QR factorization of A(p,:)
 %       b1 = cs_qleft (V, beta, p, b) ;

CSparse/MATLAB/CSparse/cs_qr.m

@@ -13,7 +13,7 @@
 %
 %   Example:
 %
-%       Prob = UFget ('HB/well1033') ; A = Prob.A ; [m n] = size (A) ;
+%       Prob = ssget ('HB/well1033') ; A = Prob.A ; [m n] = size (A) ;
 %       b = rand (m,1) ;
 %       [V,beta,p,R,q] = cs_qr (A) ; % QR factorization of A(p,q)
 %       b1 = cs_qleft (V, beta, p, b) ;

CSparse/MATLAB/CSparse/cs_qrsol.m

@@ -7,7 +7,7 @@
 %   (0: natural, 3: amd(A'*A)).  The default ordering is 3.
 %
 %   Example:
-%       Prob = UFget ('HB/well1033') ; A = Prob.A ; [m n] = size (A) ;
+%       Prob = ssget ('HB/well1033') ; A = Prob.A ; [m n] = size (A) ;
 %       b = rand (m,1) ;
 %       x1 = cs_qrsol (A,b) ;
 %       x2 = A\b ;

CSparse/MATLAB/CSparse/cs_scc.m

@@ -6,7 +6,7 @@
 %   For bipartite or rectangular graphs, use cs_scc2.
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; A = Prob.A ; [p r] = cs_scc (A) ;
+%       Prob = ssget ('HB/arc130') ; A = Prob.A ; [p r] = cs_scc (A) ;
 %       cspy (A (p,p)) ;
 %
 %   See also CS_DMPERM, DMPERM, CS_SCC2.

CSparse/MATLAB/CSparse/cs_scc2.m

@@ -12,9 +12,9 @@
 %   block is given by A(r(k):r(k+1)-1,s(k):s(k+1)-1).  A can be rectangular.
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; A = Prob.A ; [p q r s] = cs_scc2 (A) ;
+%       Prob = ssget ('HB/arc130') ; A = Prob.A ; [p q r s] = cs_scc2 (A) ;
 %       cspy (A (p,q)) ;
-%       Prob = UFget ('HB/wm1') ; A = Prob.A ; [p q r s] = cs_scc2 (A) ;
+%       Prob = ssget ('HB/wm1') ; A = Prob.A ; [p q r s] = cs_scc2 (A) ;
 %       cspy (A (p,q)) ;
 %
 %   See also CS_DMPERM, DMPERM, CS_SCC, CCSPY.

CSparse/MATLAB/CSparse/cs_sparse.m

@@ -4,7 +4,7 @@
 %   be real, and the length of i, j, and x must be the same.
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; S = Prob.A ;
+%       Prob = ssget ('HB/arc130') ; S = Prob.A ;
 %       [i j x] = find (S) ;
 %       A = cs_sparse (i,j,x) ;
 %       S-A

CSparse/MATLAB/CSparse/cs_sqr.m

@@ -13,7 +13,7 @@
 %   q is the fill-reducing ordering, if requested.
 %
 %   Example:
-%       Prob = UFget ('HB/ibm32') ; A = Prob.A ;
+%       Prob = ssget ('HB/ibm32') ; A = Prob.A ;
 %       [vnz, rnz, parent, c, leftmost, p, q] = cs_sqr (A) ;
 %       cspy (A (p,q)) ;
 %

CSparse/MATLAB/CSparse/cs_symperm.m

@@ -5,7 +5,7 @@
 %   symmetric with just their upper triangular parts stored).  A must be square.
 %
 %   Example:
-%       Prob = UFget ('HB/bcsstk01') ; A = Prob.A ;
+%       Prob = ssget ('HB/bcsstk01') ; A = Prob.A ;
 %       p = cs_amd (A) ;
 %       C = cs_symperm (A, p) ;
 %       cspy (A (p,p)) ;

CSparse/MATLAB/CSparse/cs_transpose.m

@@ -3,7 +3,7 @@
 %   C = cs_transpose(A), computes C = A' where A must be sparse and real.
 %
 %   Example:
-%       Prob = UFget ('HB/ibm32') ; A = Prob.A ;
+%       Prob = ssget ('HB/ibm32') ; A = Prob.A ;
 %       C = cs_transpose (A) ;
 %       C-A'
 %

CSparse/MATLAB/CSparse/cs_updown.m

@@ -10,7 +10,7 @@
 %   cancellation (use cs_chol(A,0)).
 %
 %   Example:
-%       Prob = UFget ('HB/bcsstk01') ; A = Prob.A ; n = size (A,1) ;
+%       Prob = ssget ('HB/bcsstk01') ; A = Prob.A ; n = size (A,1) ;
 %       L = cs_chol (A,0) ;
 %       parent = cs_etree (A) ;
 %       c = sprand (L (:, floor(n/2))) ;

CSparse/MATLAB/CSparse/cs_usolve.m

@@ -6,7 +6,7 @@
 %   returned in topological order).
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; A = Prob.A ; n = size (A,1) ;
+%       Prob = ssget ('HB/arc130') ; A = Prob.A ; n = size (A,1) ;
 %       b = rand (n,1);
 %       [L U p q] = cs_lu (A) ;
 %       x = cs_usolve (U, cs_lsolve (L, b(p))) ;   % x = U \ (L \ b(p)) ;

CSparse/MATLAB/CSparse/cs_utsolve.m

@@ -4,7 +4,7 @@
 %   zero-free diagonal.  b must be a full vector.
 %
 %   Example:
-%       Prob = UFget ('HB/arc130') ; A = Prob.A ; n = size (A,1) ;
+%       Prob = ssget ('HB/arc130') ; A = Prob.A ; n = size (A,1) ;
 %       b = rand (n,1);
 %       [L U p q] = cs_lu (A) ;
 %       x = cs_ltsolve (L, cs_utsolve (U, b(q))) ;   % x = L' \ (U' \ b(q)) ;