v4.4.6

AMD/Doc/License.txt

@@ -0,0 +1,91 @@
+AMD, Copyright (c), 1996-2015, Timothy A. Davis,
+Patrick R. Amestoy, and Iain S. Duff.  All Rights Reserved.
+
+AMD License: At the user's option, you may use AMD under either the LGPL
+version 2.1 license, or the BSD 3-clause license.  You may not use both
+licenses, nor may you mix-and-match clauses from each license.  To use a
+license, in the documentation for your application simply state either of the
+following, replacing <YOUR APPLICATION> with the name of your application:
+
+    AMD, Copyright (c), 1996-2015, Timothy A. Davis,
+    Patrick R. Amestoy, and Iain S. Duff.  All Rights Reserved.
+    Used in <YOUR APPLICATION> under the BSD 3-clause license.
+
+or
+
+    AMD, Copyright (c), 1996-2015, Timothy A. Davis,
+    Patrick R. Amestoy, and Iain S. Duff.  All Rights Reserved.
+    Used in <YOUR APPLICATION> under the LGPL v2.1 license.
+
+In the event that your package <A> includes another package <B> by another
+author, and <A> and <B> use AMD under different licenses, you may select
+one license to apply to both uses of AMD in the combined application.
+
+Availability:
+
+    http://www.suitesparse.com
+
+-------------------------------------------------------------------------------
+BSD 3-clause:
+-------------------------------------------------------------------------------
+
+    Copyright (c), 1996-2015, Timothy A. Davis,
+    Patrick R. Amestoy, and Iain S. Duff.  All Rights Reserved.
+
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+        * Redistributions of source code must retain the above copyright
+          notice, this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above copyright
+          notice, this list of conditions and the following disclaimer in the
+          documentation and/or other materials provided with the distribution.
+        * Neither the name of the organizations to which the authors are
+          affiliated, nor the names of its contributors may be used to endorse
+          or promote products derived from this software without specific prior
+          written permission.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+    AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+    IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+    ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY
+    DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+    CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+    LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+    OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+    DAMAGE.
+
+-------------------------------------------------------------------------------
+LGPL version 2.1:
+-------------------------------------------------------------------------------
+
+    Your use or distribution of AMD or any modified version of
+    AMD implies that you agree to this License.
+
+    This library is free software; you can redistribute it and/or
+    modify it under the terms of the GNU Lesser General Public
+    License as published by the Free Software Foundation; either
+    version 2.1 of the License, or (at your option) any later version.
+
+    This library is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    Lesser General Public License for more details.
+
+    You should have received a copy of the GNU Lesser General Public
+    License along with this library; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301
+    USA
+
+    Permission is hereby granted to use or copy this program under the
+    terms of the GNU LGPL, provided that the Copyright, this License,
+    and the Availability of the original version is retained on all copies.
+    User documentation of any code that uses this code or any modified
+    version of this code must cite the Copyright, this License, the
+    Availability note, and "Used by permission." Permission to modify
+    the code and to distribute modified code is granted, provided the
+    Copyright, this License, and the Availability note are retained,
+    and a notice that the code was modified is included.
+
+-------------------------------------------------------------------------------

CHOLMOD/Doc/ChangeLog

@@ -1,3 +1,9 @@
+July 14, 2015: version 3.0.6
+
+    * NGPL did not disable MatrixOps, Modify, and Supernodal modules,
+        contradicting its definition in the User Guide.  Fixed in this release.
+    * added MATLAB interface for row add/delete (lurowmod mexFunction)
+
 Jan 19, 2015: version 3.0.5
 
     * minor bug fix to cholmod_symmetry.c for the 'quick return'

CHOLMOD/Doc/Makefile

@@ -36,6 +36,7 @@ M = \
 	../MATLAB/ldlsolve.m \
 	../MATLAB/ldlsplit.m \
 	../MATLAB/ldlupdate.m \
+	../MATLAB/ldlrowmod.m \
 	../MATLAB/metis.m \
 	../MATLAB/nesdis.m \
 	../MATLAB/resymbol.m \
@@ -61,6 +62,7 @@ UserGuide.pdf: UserGuide.tex UserGuide.bib $(I) $(C) $(M) Makefile getproto rule
 	./getmproto ../MATLAB/ldlsolve.m > _ldlsolve_m.tex
 	./getmproto ../MATLAB/ldlsplit.m > _ldlsplit_m.tex
 	./getmproto ../MATLAB/ldlupdate.m > _ldlupdate_m.tex
+	./getmproto ../MATLAB/ldlrowmod.m > _ldlrowmod_m.tex
 	./getmproto ../MATLAB/metis.m > _metis_m.tex
 	./getmproto ../MATLAB/mread.m > _mread_m.tex
 	./getmproto ../MATLAB/spsym.m > _spsym_m.tex

CHOLMOD/Doc/UserGuide.tex

@@ -21,7 +21,7 @@
 \title{User Guide for CHOLMOD: a sparse Cholesky factorization and
 modification package}
 
-\date{VERSION 3.0.5, Jan 19, 2015}
+\date{VERSION 3.0.6, July 14, 2015}
 \maketitle
 
 %-------------------------------------------------------------------------------
@@ -329,7 +329,9 @@
 \item {\tt -DCAMD}:   do not include the interfaces to CAMD, CCOLAMD,
 and CSYMAMD in the Partition module.   License: GNU LGPL.
 \item {\tt -DNGPL}:	    do not include any GNU GPL Modules in the CHOLMOD library.
+Note that the Demo requires the MatrixOps module.
 \item {\tt -DNMATRIXOPS}:   do not include the MatrixOps module.   License: GNU GPL.
+Note that the Demo requires the MatrixOps module.
 \item {\tt -DNMODIFY}:	    do not include the Modify module.      License: GNU GPL.
 \item {\tt -DNSUPERNODAL}:  do not include the Supernodal module.  License: GNU GPL.
 \item {\tt -DNPRINT}:	    do not print anything.
@@ -397,6 +399,7 @@
 {\tt ldlsolve}	    & {\tt x = L'}$\backslash${\tt (D}$\backslash${\tt (L}$\backslash${\tt b))} \\
 {\tt ldlsplit}	    & split the output of {\tt ldlchol} into {\tt L} and {\tt D} \\
 {\tt ldlupdate}	    & update/downdate an {\tt L*D*L'} factorization \\
+{\tt ldlrowmod}	    & add/delete a row from an {\tt L*D*L'} factorization \\
 {\tt metis}	    & interface to {\tt METIS\_NodeND} ordering \\
 {\tt mread}	    & read a sparse or dense Matrix Market file \\
 {\tt mwrite}	    & write a sparse or dense Matrix Market file \\
@@ -434,6 +437,8 @@ \subsection{{\tt ldlsplit}: split an $\m{LDL}\tr$ factorization}		\input{_ldlspl
 \newpage
 \subsection{{\tt ldlupdate}: update/downdate an $\m{LDL}\tr$ factorization}	\input{_ldlupdate_m.tex}
 \newpage
+\subsection{{\tt ldlrowmod}: add/delete a row from an $\m{LDL}\tr$ factorization}	\input{_ldlrowmod_m.tex}
+\newpage
 \subsection{{\tt mread}: read a sparse or dense matrix from a Matrix Market file}\input{_mread_m.tex}
 \subsection{{\tt mwrite}: write a sparse or dense matrix to a Matrix Market file}	\input{_mwrite_m.tex}
 \newpage

CHOLMOD/Include/cholmod_core.h

@@ -246,11 +246,11 @@
 
 #define CHOLMOD_HAS_VERSION_FUNCTION
 
-#define CHOLMOD_DATE "Jan 7, 2015"
+#define CHOLMOD_DATE "July 14, 2015"
 #define CHOLMOD_VER_CODE(main,sub) ((main) * 1000 + (sub))
 #define CHOLMOD_MAIN_VERSION 3
 #define CHOLMOD_SUB_VERSION 0
-#define CHOLMOD_SUBSUB_VERSION 5
+#define CHOLMOD_SUBSUB_VERSION 6
 #define CHOLMOD_VERSION \
     CHOLMOD_VER_CODE(CHOLMOD_MAIN_VERSION,CHOLMOD_SUB_VERSION)
 

CHOLMOD/MATLAB/Contents.m

@@ -5,6 +5,7 @@
 %   lchol           - sparse A=L*L' factorization.
 %   ldlchol         - sparse A=LDL' factorization
 %   ldlupdate       - multiple-rank update or downdate of a sparse LDL' factorization.
+%   ldlrowmod       - add/delete row from a sparse LDL' factorization.
 %   resymbol        - recomputes the symbolic Cholesky factorization of the matrix A.
 %   ldlsolve        - solve LDL'x=b using a sparse LDL' factorization
 %   ldlsplit        - split an LDL' factorization into L and D.
@@ -25,6 +26,7 @@
 %   cholmod_install - compile and install CHOLMOD, AMD, COLAMD, CCOLAMD, CAMD
 %   cholmod_make    - compiles the CHOLMOD mexFunctions
 %   graph_demo      - graph partitioning demo
+%   cholmod_updown_demo - a demo of update/downdate and row add/delete functions
 %
 %
 % Example:
@@ -33,4 +35,4 @@
 % Note: cholmod has been renamed cholmod2, so as not to conflict with itself
 % (the MATLAB built-in cholmod function).
 
-%   Copyright 2006-2007, Timothy A. Davis, http://www.suitesparse.com
+%   Copyright 2006-2015, Timothy A. Davis, http://www.suitesparse.com

CHOLMOD/MATLAB/Test/cholmod_test.m

@@ -13,6 +13,7 @@ function cholmod_test (nmat, do_diary)
 % do_diary: 1 to save results in a diary, 0 otherwise.  Default 0.
 %
 % cholmod_demo: run tests on a few random matrices
+% cholmod_updown_demo: run tests for update/downdate and row add/delete
 % graph_demo: graph partitioning demo
 % test0:  test most CHOLMOD functions
 % test1:  test sparse2
@@ -112,7 +113,8 @@ function cholmod_test (nmat, do_diary)
 
 try
 
-    cholmod_demo                    ; waitbar ( 1/tt, h, 'CHOLMOD graph demo');
+    cholmod_demo                    ; waitbar ( 1/tt, h, 'CHOLMOD up/down demo');
+    cholmod_update_demo             ; waitbar ( 1/tt, h, 'CHOLMOD graph demo');
     if (do_metis)
         graph_demo ;
     end

CHOLMOD/MATLAB/Test/test0.m

@@ -206,7 +206,6 @@ function test0 (nmat)
 	else
 	    fprintf ('  no fill-in\n') ;
 	end
-	clear LD
 
 	% check the factorization, LD2 has LDL' factorization of S+C*C'
 	[L,D] = ldlsplit (LD2) ;
@@ -275,11 +274,52 @@ function test0 (nmat)
 	err2 = norm (S2*x-b,1) / norm (S,1) ;
 	fprintf ('MATLAB  residual:  %6.1e (sparse b)\n', err2) ;
 
+        % ----------------------------------------------------------------------
+        % test the row delete
+        k = max (1, fix (n/2)) ;
+        tic
+        LD6 = ldlrowmod (LD,k) ;
+        t6 = toc ;
+	fprintf ('\nCHOLMOD time: ldlrowmod, delete    %10.4f  nnz(L) %d', ...
+	    t6, nnz (LD6)) ;
+
+        I = speye (n) ;
+        S2 = S ;
+        S2 (k,:) = I (k,:) ;
+        S2 (:,k) = I (:,k) ;
+
+	% check the factorization, LD6 has LDL' factorization of S2
+	[L,D] = ldlsplit (LD6) ;
+	err = ldl_normest (S2, L, D) / lnorm ;
+	if (err > 1e-6)
+	    error ('!') ;
+	end
+
+        % test the row add, by adding the row back in again
+        Ck = S (:,k) ;
+        S2 (:,k) = Ck ;
+        S2 (k,:) = Ck' ;
+
+        tic
+        LD7 = ldlrowmod (LD6,k,Ck) ;
+        t7 = toc ;
+	fprintf ('\nCHOLMOD time: ldlrowmod, add       %10.4f  nnz(L) %d', ...
+	    t7, nnz (LD7)) ;
+
+	% check the factorization, LD7 has LDL' factorization of S
+	[L,D] = ldlsplit (LD7) ;
+	err = ldl_normest (S, L, D) / lnorm ;
+	if (err > 1e-6)
+	    error ('!') ;
+	end
+
+        % ----------------------------------------------------------------------
+
     % catch
     %	fprintf ('failed\n') ;
     % end
 
-    clear A S C L R LD LD2 LD3 D p q C1 C2 LD3 S2 LD4 b x LD5
+    clear A S C L R LD LD2 LD3 D p q C1 C2 LD3 S2 LD4 b x LD5 I LDL6 LD7 Ck
 
 end
 

CHOLMOD/MATLAB/cholmod_demo.m

@@ -115,15 +115,35 @@ function try_matrix (A)
     t2, 1e-6 * fl / t2) ;
 
 tic
-LD = ldlupdate (LD,C) ;
+LD2 = ldlupdate (LD,C) ;
 t3 = toc ;
 fprintf ('CHOLMOD ldlupdate(sparse(A),C) time: %6.2f (rank-1, C dense)\n', t3) ;
 
-[L,D] = ldlsplit (LD) ;
-L = full (L) ;
+[L,D] = ldlsplit (LD2) ;
+% L = full (L) ;
 err = norm ((S+C*C') - L*D*L', 1) / norm (S,1) ;
 fprintf ('err: %g\n', err) ;
 
+k = max (1,fix(n/2))  ;
+tic
+LD3 = ldlrowmod (LD, k) ;
+t4 = toc ;
+fprintf ('CHOLMOD ldlrowmod(LD,k)        time: %6.2f\n', t4) ;
+
+[L,D] = ldlsplit (LD3) ;
+S2 = S ;
+I = speye (n) ;
+S2 (k,:) = I (k,:) ;
+S2 (:,k) = I (:,k) ;
+err = norm (S2 - L*D*L', 1) / norm (S,1) ;
+fprintf ('err: %g\n', err) ;
+
+LD4 = ldlchol (S2) ;
+[L,D] = ldlsplit (LD4) ;
+% L = full (L) ;
+err = norm (S2 - L*D*L', 1) / norm (S,1) ;
+fprintf ('err: %g\n', err) ;
+
 tic
 R = chol (S) ;		    %#ok
 s1 = toc ;

CHOLMOD/MATLAB/cholmod_install.m

@@ -16,9 +16,9 @@ function cholmod_install (metis_path)
 %
 % See also analyze, bisect, chol2, cholmod2, etree2, lchol, ldlchol, ldlsolve,
 %   ldlupdate, metis, spsym, nesdis, septree, resymbol, sdmult, sparse2,
-%   symbfact2, mread, mwrite, amd2, colamd2, camd, ccolamd
+%   symbfact2, mread, mwrite, amd2, colamd2, camd, ccolamd, ldlrowmod
 
-%   Copyright 2006-2007, Timothy A. Davis
+%   Copyright 2006-2015, Timothy A. Davis
 
 if (nargin < 1)
     metis_path = '../../metis-4.0' ;

CHOLMOD/MATLAB/cholmod_make.m

@@ -15,9 +15,9 @@ function cholmod_make (metis_path)
 %
 % See also analyze, bisect, chol2, cholmod2, etree2, lchol, ldlchol, ldlsolve,
 %   ldlupdate, metis, spsym, nesdis, septree, resymbol, sdmult, sparse2,
-%   symbfact2, mread, mwrite
+%   symbfact2, mread, mwrite, ldlrowmod
 
-%   Copyright 2006-2007, Timothy A. Davis, http://www.suitesparse.com
+%   Copyright 2006-2015, Timothy A. Davis, http://www.suitesparse.com
 
 details = 0 ;	    % 1 if details of each command are to be printed
 
@@ -283,6 +283,7 @@ function cholmod_make (metis_path)
     'ldlchol', ...
     'ldlsolve', ...
     'ldlupdate', ...
+    'ldlrowmod', ...
     'metis', ...
     'spsym', ...
     'nesdis', ...