v4.4.4

CHOLMOD/Doc/ChangeLog

@@ -1,4 +1,9 @@
-Jan 7, 2017: version 3.0.4
+Jan 19, 2015: version 3.0.5
+
+    * minor bug fix to cholmod_symmetry.c for the 'quick return'
+        (option == 0).
+
+Jan 7, 2015: version 3.0.4
 
     * serious bug fix to supernodal factorization.  The bug was introduced in
 	CHOLMOD v3.0.0 when the GPU acceleration was given a major update.

CHOLMOD/Doc/UserGuide.tex

@@ -21,7 +21,7 @@
 \title{User Guide for CHOLMOD: a sparse Cholesky factorization and
 modification package}
 
-\date{VERSION 3.0.4, Jan 7, 2015}
+\date{VERSION 3.0.5, Jan 19, 2015}
 \maketitle
 
 %-------------------------------------------------------------------------------
@@ -47,7 +47,7 @@
 \end{abstract}
 %-------------------------------------------------------------------------------
 
-CHOLMOD Copyright\copyright 2005-2014 by Timothy A. Davis.  Portions are also
+CHOLMOD Copyright\copyright 2005-2015 by Timothy A. Davis.  Portions are also
 copyrighted by William W. Hager (the {\tt Modify} Module),
 and the University of Florida (the {\tt Partition} and {\tt Core} Modules).
 All Rights Reserved.  Some of CHOLMOD's Modules are distributed under the GNU

CHOLMOD/Include/cholmod_core.h

@@ -250,7 +250,7 @@
 #define CHOLMOD_VER_CODE(main,sub) ((main) * 1000 + (sub))
 #define CHOLMOD_MAIN_VERSION 3
 #define CHOLMOD_SUB_VERSION 0
-#define CHOLMOD_SUBSUB_VERSION 4
+#define CHOLMOD_SUBSUB_VERSION 5
 #define CHOLMOD_VERSION \
     CHOLMOD_VER_CODE(CHOLMOD_MAIN_VERSION,CHOLMOD_SUB_VERSION)
 

CHOLMOD/MATLAB/Test/cholmod_test.m

@@ -106,7 +106,7 @@ function cholmod_test (nmat, do_diary)
     do_metis = 0 ;
 end
 
-tt = 34 ;
+tt = 35 ;
 
 h = waitbar (0.5/tt, 'CHOLMOD demo:') ;
 
@@ -167,6 +167,7 @@ function cholmod_test (nmat, do_diary)
 
     ltest                           ; waitbar (32/tt, h, 'CHOLMOD ltest') ;
     lxtest                          ; waitbar (33/tt, h, 'CHOLMOD lxtest') ;
+    test29                          ; waitbar (34/tt, h, 'CHOLMOD test29') ;
 
     waitbar (tt/tt, h, 'CHOLMOD test done') ;
     fprintf ('=============================================================\n');

CHOLMOD/MATLAB/Test/test29.m

@@ -0,0 +1,141 @@
+function test29
+%TEST29 test spsym
+% Example:
+%   spsym
+% See also cholmod_test
+
+% Copyright 2015, Timothy A. Davis, http://www.suitesparse.com
+
+rand ('state', 0) ;
+
+r = zeros (0,2) ;
+for n = 0:5
+
+    % real unsymmetric, diagonal all nonzero
+    A = sparse (rand (n,n)) ;
+    r = [r ; test_spsym(A)] ;
+
+    % real symmetric, diagonal all nonzero
+    A = A+A' ;
+    r = [r ; test_spsym(A)] ;
+
+    % real unsymmetric, diagonal all nonzero
+    A (2,1) = 0 ;
+    r = [r ; test_spsym(A)] ;
+
+    % real symmetric, diagonal all zero
+    A = sparse (n,n) ;
+    r = [r ; test_spsym(A)] ;
+
+    % real symmetric, diagonal all nonzero
+    A = speye (n,n) ;
+    r = [r ; test_spsym(A)] ;
+
+    % real symmetric, diagonal mostly nonzero
+    A (2,2) = 0 ;
+    r = [r ; test_spsym(A)] ;
+
+    % real rectangular, or square unsymmetric
+    for m = 0:5
+        A = sparse (rand (n,m)) ;
+        r = [r ; test_spsym(A)] ;
+    end
+
+    % skew symmetric when n > 1
+    A = tril (sparse (rand (n,n)), -1) ;
+    A = A-A' ;
+    c = test_spsym(A) ;
+    r = [r ; c ] ;
+
+    % complex Hermitian (when n > 1)
+    A = sparse (rand (n,n)) + 1i * sparse (rand (n,n)) ;
+    A = A+A' ;
+    c = test_spsym(A) ;
+    r = [r ; c ] ;
+
+    % complex Hermitian but with non-positive diagonal (when n > 1)
+    A (3,3) = -1 ;
+    c = test_spsym(A) ;
+    r = [r ; c] ;
+
+end
+
+r = unique (r, 'rows') ;
+rtrue =  [
+     1     1
+     2     2
+     3     2
+     4     2
+     5     2
+     6     6
+     7     7 ] ;
+if (~isequal (r, rtrue))
+    error ('failed.  Incomplete test cases') ;
+end
+
+% test with the UF sparse matrix collection
+r = zeros (0,2) ;
+index = UFget ;
+for i = [168 27 2137 56 231 1621 -1621] ;
+    Prob = UFget (abs (i),index)
+    A = Prob.A ;
+    if (i < 0)
+        % UF collection does not contain any matrices for which spsym(A) = 4.
+        % (complex Hermitian with zero nonpos. diagonal).  So make one.
+        fprintf ('setting A (5,5) = 0\n') ;
+        A (5,5) = 0 ;
+    end
+    c = test_spsym (A) ;
+    c
+    fprintf ('full  test:') ; print_result (c (1)) ;
+    fprintf ('quick test:') ; print_result (c (2)) ;
+    r = [r ; c] ;
+end
+
+r = unique (r, 'rows') ;
+if (~isequal (r, rtrue))
+    error ('failed.  Incomplete test cases') ;
+end
+
+%-------------------------------------------------------------------------------
+
+function r = test_spsym (A)
+s1 = spsym (A) ;
+s2 = get_symmetry (A) ;
+if (s1 ~= s2)
+    error ('failed!')
+end
+s3 = spsym (A,0) ;
+s4 = get_symmetry (A,0) ;
+if (s3 ~= s1 || s4 ~= s1)
+    error ('failed!')
+end
+s5 = spsym (A,1) ;
+s6 = get_symmetry (A,1) ;
+if (s5 ~= s6)
+    error ('failed!')
+end
+r = [s1 s5] ;   % r(1) is the full test, r(2) is the quick test
+
+%-------------------------------------------------------------------------------
+
+function print_result (s)
+switch (s)
+case 1
+    fprintf ('rectangular\n') ;
+case 2
+    fprintf ('unsymmetric (or not Cholesky candidate for quick test)\n') ;
+case 3
+    fprintf ('symmetric, but with one or more A(j,j) <= 0\n') ;
+case 4
+    fprintf ('Hermitian, but with one or more A(j,j) <= 0 or with nonzero imaginary part\n') ;
+case 5
+    fprintf ('skew symmetric\n') ;
+case 6
+    fprintf ('symmetric with real positive diagonal\n') ;
+case 7
+    fprintf ('Hermitian with real positive diagonal\n') ;
+otherwise
+    error ('unknown result') ;
+end
+

CHOLMOD/Makefile

@@ -2,7 +2,7 @@
 # CHOLMOD Makefile
 #-------------------------------------------------------------------------------
 
-VERSION = 3.0.3
+VERSION = 3.0.5
 
 # Note: If you do not have METIS, or do not wish to use it in CHOLMOD, you must
 # compile CHOLMOD with the -DNPARTITION flag.

CHOLMOD/MatrixOps/cholmod_symmetry.c

@@ -441,7 +441,7 @@ int CHOLMOD(symmetry)
 	/* quick return if not Cholesky candidate */
 	/* ------------------------------------------------------------------ */
 
-	if (option < 1 && (!posdiag || nzdiag < ncol))
+	if (option < 1 && (!posdiag || nzdiag <= j))
 	{
 	    /* Diagonal entry not present, or present but negative or with
 	     * nonzero imaginary part.  Quick return for option 0. */

CHOLMOD/Tcov/Makefile

@@ -23,6 +23,9 @@ CC = gcc
 # to test with everthing
 C = $(CC) $(CF) $(CHOLMOD_CONFIG) $(NANTESTS)
 
+# default LAPACK and BLAS from SuiteSparse_config.mk:
+  LIB = $(METIS) -lm $(LAPACK) $(BLAS)
+
 # optimized LAPACK and BLAS
 # LIB = $(METIS) -lm $(LAPACK) $(BLAS) $(XERBLA) -L/shared/apps/rhel-6.2/intel/ics-2013/lib/intel64 -liomp5
 
@@ -31,7 +34,7 @@ C = $(CC) $(CF) $(CHOLMOD_CONFIG) $(NANTESTS)
 # LIB = $(METIS) -lm -llapack_plain -lblas_plain -lgfortran -lgfortranbegin
 # LIB = $(METIS) -lm -llapack -lblas -lgfortran -lgfortranbegin
 # Linux:
-  LIB = $(METIS) -lm -llapack_plain -lblas_plain -lgfortran -lgfortranbegin -lpthread -lrt
+# LIB = $(METIS) -lm -llapack_plain -lblas_plain -lgfortran -lgfortranbegin -lpthread -lrt
 # Mac:
 # LIB = $(METIS) -lm -llapack -lblas -lgfortran -lgfortranbegin -lpthread
 

CHOLMOD/Tcov/tmp/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

CHOLMOD/Valgrind/tmp/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

CSparse/MATLAB/UFget/MM/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

CSparse/MATLAB/UFget/RB/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

CSparse/MATLAB/UFget/svd/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

CXSparse/MATLAB/UFget/MM/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

CXSparse/MATLAB/UFget/RB/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

CXSparse/MATLAB/UFget/svd/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

ChangeLog

@@ -1,3 +1,15 @@
+Mar 24, 2015: SuiteSparse version 4.4.4
+
+    * CHOLMOD version number corrected.  In 4.4.3, the CHOLMOD_SUBSUB_VERSION
+        string was left at '4' (it should have been '5', for CHOLMOD 3.0.5).
+        This version of SuiteSparse corrects this glitch.
+    * Minor changes to comments in SuiteSparse_config.
+    * SPQR version 2.0.1 released (minor update to documentation)
+
+Jan 19, 2015: SuiteSparse version 4.4.3
+
+    * CHOLMOD 3.0.5: minor bug fix to MatrixOps/cholmod_symmetry
+
 Jan 7, 2015: SuiteSparse version 4.4.2
 
     * CHOLMOD 3.0.4: serious bug fix in supernodal factorization,

README.txt

@@ -1,6 +1,6 @@
 SuiteSparse:  A Suite of Sparse matrix packages at http://www.suitesparse.com
 
-Jan 7, 2015.  SuiteSparse VERSION 4.4.2
+March 24, 2015.  SuiteSparse VERSION 4.4.4
 
 ------------------
 SuiteSparse/README

SPQR/Demo/Makefile

@@ -195,7 +195,7 @@ purge: distclean
 	- $(RM) -r *.dot pfile tfile
 
 distclean: clean
-	- $(RM) qrdemo qrdemo_gpu qrdemoc qrsimple qrsimplec
+	- $(RM) qrdemo qrdemo_gpu qrdemoc qrsimple qrsimplec X.mtx
 	- $(RM) -r *.dSYM gpu_results.txt qrdemo_gpu2 qrdemo_gpu3
 
 clean:

SPQR/Demo/README.txt

@@ -31,6 +31,7 @@ demo_colamd*.sh     scripts for running the GPU demo with COLAMD
 demo_metis*.sh      scripts for running the GPU demo with METIS
 go*.m               MATLAB scripts for testing the GPU version
 qrdemo_gpu*.cpp     GPU demos
+qrdemo_gpu.out      output of qrdemo_gpu.cpp
 
 --------------------------------------------------------------------------------
 

SPQR/Demo/qrdemo_gpu.out

@@ -0,0 +1,18 @@
+./qrdemo_gpu  ../Matrix/west0067.mtx 2
+available GPU memory: 11160.8 MB, warmup time: 0.376328
+Matrix     67-by-67     nnz:    294
+
+norm(Ax-b):  4.6e-17
+norm(A'(Ax-b))          1.6e-14 rank: 67 of 67
+./qrdemo_gpu  ../Matrix/lp_e226_transposed.mtx 2
+available GPU memory: 11160.8 MB, warmup time: 0.372199
+Matrix    472-by-223    nnz:   2768
+
+norm(Ax-b):  9.2e+00
+norm(A'(Ax-b))          2.1e-10 rank: 223 of 223
+./qrdemo_gpu  ../Matrix/lp_e226_transposed.mtx 6
+available GPU memory: 11160.8 MB, warmup time: 0.36664
+Matrix    472-by-223    nnz:   2768
+
+norm(Ax-b):  9.2e+00
+norm(A'(Ax-b))          4.4e-10 rank: 223 of 223

SPQR/Doc/ChangeLog

@@ -1,3 +1,7 @@
+Mar 24, 2015: version 2.0.1
+
+    * minor changes to documentation
+
 Oct 17, 2014: version 2.0.0
 
     * MAJOR UPDATE:  added GPU support.  Up to 11x faster than CPU version.

SPQR/Doc/spqr_user_guide.tex

@@ -29,7 +29,7 @@
 Science Foundation, under grants 0203270, 0620286, and 0619080.},
 Sencer Nuri Yeralan, and Sanjay Ranka}
 
-\date{VERSION 2.0.0, Oct 17, 2014}
+\date{VERSION 2.0.1, March 24, 2015}
 
 %-------------------------------------------------------------------------------
 \begin{document}
@@ -902,10 +902,6 @@ \section{GPU acceleration}
 GPU acceleration is not yet available via the MATLAB mexFunction interface. 
 We expect to include this in a future release.
 
-This GPU acceleration in SuiteSparseQR has been heavily tested and we feel that
-it is now polished enough to appear in SuiteSparse.  However, we are also
-actively developing this code, so future enhancements are expected.
-
 For a detailed technical report on the GPU-accelerated algorithm,
 see \verb'qrgpu_paper.pdf' in the \verb'Doc' directory.
 

SPQR/Include/SuiteSparseQR_definitions.h

@@ -59,11 +59,11 @@
         #endif
  */
 
-#define SPQR_DATE "Oct 1, 2014"
+#define SPQR_DATE "Mar 24, 2015"
 #define SPQR_VER_CODE(main,sub) ((main) * 1000 + (sub))
 #define SPQR_MAIN_VERSION 2
 #define SPQR_SUB_VERSION 0
-#define SPQR_SUBSUB_VERSION 0
+#define SPQR_SUBSUB_VERSION 1
 #define SPQR_VERSION SPQR_VER_CODE(SPQR_MAIN_VERSION,SPQR_SUB_VERSION)
 
 #endif

SPQR/Makefile

@@ -2,7 +2,7 @@
 # SuiteSparseQR Makefile
 #-------------------------------------------------------------------------------
 
-VERSION = 2.0.0
+VERSION = 2.0.1
 
 include ../SuiteSparse_config/SuiteSparse_config.mk