As of SuiteSparse 4.5.6 CCOLAMD is now licensed under BSD-3!

LICENSE

@@ -4,11 +4,11 @@ LICENSE.BSD in this directory.
 GTSAM contains two third party libraries, with documentation of licensing and 
 modifications as follows:
 
-- CCOLAMD 2.73: Tim Davis' constrained column approximate minimum degree 
+- CCOLAMD 2.9.3: Tim Davis' constrained column approximate minimum degree 
 ordering library
     - Included unmodified in gtsam/3rdparty/CCOLAMD and gtsam/3rdparty/UFconfig
-    - http://www.cise.ufl.edu/research/sparse
+    - http://faculty.cse.tamu.edu/davis/suitesparse.html
-    - Licenced under LGPL v2.1, provided in gtsam/3rdparty/CCOLAMD/Doc/lesser.txt
+    - Licenced under BSD-3, provided in gtsam/3rdparty/CCOLAMD/Doc/License.txt
 - Eigen 3.2:  General C++ matrix and linear algebra library
     - Modified with 3 patches that have been contributed back to the Eigen team:
         - http://eigen.tuxfamily.org/bz/show_bug.cgi?id=704 (Householder QR MKL selection)

gtsam/3rdparty/CCOLAMD/Demo/ccolamd_example.out

@@ -15,7 +15,7 @@ Column 3, with 2 entries:
     row 1
     row 3
 
-ccolamd version 2.9, Apr 1, 2016: OK.  
+ccolamd version 2.9, May 4, 2016: OK.  
 ccolamd: number of dense or empty rows ignored:    0
 ccolamd: number of dense or empty columns ignored: 0
 ccolamd: number of garbage collections performed:  0
@@ -38,7 +38,7 @@ Column 3, with 1 entries:
     row 4
 Column 4, with 0 entries:
 
-csymamd version 2.9, Apr 1, 2016: OK.  
+csymamd version 2.9, May 4, 2016: OK.  
 csymamd: number of dense or empty rows ignored:    0
 csymamd: number of dense or empty columns ignored: 0
 csymamd: number of garbage collections performed:  0

gtsam/3rdparty/CCOLAMD/Demo/ccolamd_l_example.out

@@ -15,7 +15,7 @@ Column 3, with 2 entries:
     row 1
     row 3
 
-ccolamd version 2.9, Apr 1, 2016: OK.  
+ccolamd version 2.9, May 4, 2016: OK.  
 ccolamd: number of dense or empty rows ignored:    0
 ccolamd: number of dense or empty columns ignored: 0
 ccolamd: number of garbage collections performed:  0
@@ -38,7 +38,7 @@ Column 3, with 1 entries:
     row 4
 Column 4, with 0 entries:
 
-csymamd version 2.9, Apr 1, 2016: OK.  
+csymamd version 2.9, May 4, 2016: OK.  
 csymamd: number of dense or empty rows ignored:    0
 csymamd: number of dense or empty columns ignored: 0
 csymamd: number of garbage collections performed:  0

gtsam/3rdparty/CCOLAMD/Demo/my_ccolamd_example.out

@@ -1,50 +0,0 @@
-ccolamd 5-by-4 input matrix:
-Column 0, with 3 entries:
-    row 0
-    row 1
-    row 4
-Column 1, with 2 entries:
-    row 2
-    row 4
-Column 2, with 4 entries:
-    row 0
-    row 1
-    row 2
-    row 3
-Column 3, with 2 entries:
-    row 1
-    row 3
-
-ccolamd version 2.7, Jan 25, 2011: OK.  
-ccolamd: number of dense or empty rows ignored:    0
-ccolamd: number of dense or empty columns ignored: 0
-ccolamd: number of garbage collections performed:  0
-ccolamd column ordering:
-1st column: 1
-2nd column: 0
-3rd column: 3
-4th column: 2
-
-
-csymamd 5-by-5 input matrix:
-Entries in strictly lower triangular part:
-Column 0, with 1 entries:
-    row 1
-Column 1, with 2 entries:
-    row 2
-    row 3
-Column 2, with 0 entries:
-Column 3, with 1 entries:
-    row 4
-Column 4, with 0 entries:
-
-csymamd version 2.7, Jan 25, 2011: OK.  
-csymamd: number of dense or empty rows ignored:    0
-csymamd: number of dense or empty columns ignored: 0
-csymamd: number of garbage collections performed:  0
-csymamd column ordering:
-1st row/column: 0
-2nd row/column: 2
-3rd row/column: 1
-4th row/column: 3
-5th row/column: 4

gtsam/3rdparty/CCOLAMD/Demo/my_ccolamd_l_example.out

@@ -1,50 +0,0 @@
-ccolamd 5-by-4 input matrix:
-Column 0, with 3 entries:
-    row 0
-    row 1
-    row 4
-Column 1, with 2 entries:
-    row 2
-    row 4
-Column 2, with 4 entries:
-    row 0
-    row 1
-    row 2
-    row 3
-Column 3, with 2 entries:
-    row 1
-    row 3
-
-ccolamd version 2.7, Jan 25, 2011: OK.  
-ccolamd: number of dense or empty rows ignored:    0
-ccolamd: number of dense or empty columns ignored: 0
-ccolamd: number of garbage collections performed:  0
-ccolamd_l column ordering:
-1st column: 1
-2nd column: 0
-3rd column: 3
-4th column: 2
-
-
-csymamd_l 5-by-5 input matrix:
-Entries in strictly lower triangular part:
-Column 0, with 1 entries:
-    row 1
-Column 1, with 2 entries:
-    row 2
-    row 3
-Column 2, with 0 entries:
-Column 3, with 1 entries:
-    row 4
-Column 4, with 0 entries:
-
-csymamd version 2.7, Jan 25, 2011: OK.  
-csymamd: number of dense or empty rows ignored:    0
-csymamd: number of dense or empty columns ignored: 0
-csymamd: number of garbage collections performed:  0
-csymamd_l column ordering:
-1st row/column: 0
-2nd row/column: 2
-3rd row/column: 1
-4th row/column: 3
-5th row/column: 4

gtsam/3rdparty/CCOLAMD/Doc/ChangeLog

@@ -1,3 +1,7 @@
+May 4, 2016: version 2.9.6
+
+    * minor changes to Makefile
+
 Apr 1, 2016: version 2.9.5
 
     * licensing simplified (no other change); refer to CCOLAMD/Doc/License.txt

gtsam/3rdparty/CCOLAMD/Doc/License.txt

@@ -6,16 +6,28 @@ http://www.suitesparse.com
 
 --------------------------------------------------------------------------------
 
-CCOLAMD is free software; you can redistribute it and/or
+CCOLAMD license: BSD 3-clause:
-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.
 
-CCOLAMD is distributed in the hope that it will be useful,
+    Redistribution and use in source and binary forms, with or without
-but WITHOUT ANY WARRANTY; without even the implied warranty of
+    modification, are permitted provided that the following conditions are met:
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+        * Redistributions of source code must retain the above copyright
-Lesser General Public License for more details.
+          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.
 
-You should have received a copy of the GNU Lesser General Public
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-License along with this Module; if not, write to the Free Software
+    AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+    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.

gtsam/3rdparty/CCOLAMD/Include/ccolamd.h

@@ -41,11 +41,11 @@ extern "C" {
  *	#endif
  */
 
-#define CCOLAMD_DATE "Apr 1, 2016"
+#define CCOLAMD_DATE "May 4, 2016"
 #define CCOLAMD_VERSION_CODE(main,sub) ((main) * 1000 + (sub))
 #define CCOLAMD_MAIN_VERSION 2
 #define CCOLAMD_SUB_VERSION 9
-#define CCOLAMD_SUBSUB_VERSION 5
+#define CCOLAMD_SUBSUB_VERSION 6
 #define CCOLAMD_VERSION \
 	CCOLAMD_VERSION_CODE(CCOLAMD_MAIN_VERSION,CCOLAMD_SUB_VERSION)
 

gtsam/3rdparty/CCOLAMD/Lib/Makefile

@@ -3,7 +3,7 @@
 #-------------------------------------------------------------------------------
 
 LIBRARY = libccolamd
-VERSION = 2.9.5
+VERSION = 2.9.6
 SO_VERSION = 2
 
 default: library
@@ -32,6 +32,8 @@ ccolamd_l.o: $(SRC) $(INC)
 	$(CC) $(CF) $(I) -c ../Source/ccolamd.c -DDLONG -o ccolamd_l.o
 
 # creates libccolamd.a, a C-callable CCOLAMD library
+static: $(AR_TARGET)
+
 $(AR_TARGET):  $(OBJ)
 	$(ARCHIVE)  $@ $^
 	- $(RANLIB) $@ 

gtsam/3rdparty/CCOLAMD/Makefile

@@ -20,6 +20,10 @@ all:
 library:
 	( cd Lib    ; $(MAKE) )
 
+# compile the static libraries only
+static:
+	( cd Lib    ; $(MAKE) static )
+
 # remove object files, but keep the compiled programs and library archives
 clean:
 	( cd Lib    ; $(MAKE) clean )

gtsam/3rdparty/CCOLAMD/Source/ccolamd_global.c

@@ -1,28 +0,0 @@
-/* ========================================================================== */
-/* === ccolamd_global.c ===================================================== */
-/* ========================================================================== */
-
-/* ----------------------------------------------------------------------------
- * CCOLAMD Copyright (C), Univ. of Florida.  Authors: Timothy A. Davis,
- * Sivasankaran Rajamanickam, and Stefan Larimore
- * See License.txt for the Version 2.1 of the GNU Lesser General Public License
- * http://www.cise.ufl.edu/research/sparse
- * -------------------------------------------------------------------------- */
-
-/* Global variables for CCOLAMD */
-
-#ifndef NPRINT
-#ifdef MATLAB_MEX_FILE
-#include <stdlib.h>
-#include <stdint.h>
-typedef uint16_t char16_t;
-#include "mex.h"
-int (*ccolamd_printf) (const char *, ...) = mexPrintf ;
-#else
-#include <stdio.h>
-int (*ccolamd_printf) (const char *, ...) = printf ;
-#endif
-#else
-int (*ccolamd_printf) (const char *, ...) = ((void *) 0) ;
-#endif
-

gtsam/3rdparty/SuiteSparse_config/Makefile

@@ -7,7 +7,7 @@ export SUITESPARSE
 
 # version of SuiteSparse_config is also version of SuiteSparse meta-package
 LIBRARY = libsuitesparseconfig
-VERSION = 4.5.2
+VERSION = 4.5.6
 SO_VERSION = 4
 
 default: library
@@ -27,6 +27,8 @@ OBJ = SuiteSparse_config.o
 SuiteSparse_config.o: SuiteSparse_config.c SuiteSparse_config.h
 	$(CC) $(CF) -c SuiteSparse_config.c
 
+static: $(AR_TARGET)
+
 $(AR_TARGET): $(OBJ)
 	$(ARCHIVE) $(AR_TARGET) SuiteSparse_config.o
 	$(RANLIB) $(AR_TARGET)

gtsam/3rdparty/SuiteSparse_config/README.txt

@@ -1,4 +1,4 @@
-SuiteSparse_config, 2016, Timothy A. Davis, http://www.suitesparse.com
+SuiteSparse_config, 2017, Timothy A. Davis, http://www.suitesparse.com
 (formerly the UFconfig package)
 
 This directory contains a default SuiteSparse_config.mk file.  It tries to

gtsam/3rdparty/SuiteSparse_config/SuiteSparse_config.h

@@ -184,24 +184,24 @@ int SuiteSparse_divcomplex
  *
  * SuiteSparse contains the following packages:
  *
- *  SuiteSparse_config version 4.5.2 (version always the same as SuiteSparse)
+ *  SuiteSparse_config version 4.5.6 (version always the same as SuiteSparse)
- *  AMD             version 2.4.5
+ *  AMD             version 2.4.6
- *  BTF             version 1.2.5
+ *  BTF             version 1.2.6
- *  CAMD            version 2.4.5
+ *  CAMD            version 2.4.6
- *  CCOLAMD         version 2.9.5
+ *  CCOLAMD         version 2.9.6
- *  CHOLMOD         version 3.0.10
+ *  CHOLMOD         version 3.0.11
- *  COLAMD          version 2.9.5
+ *  COLAMD          version 2.9.6
- *  CSparse         version 3.1.8
+ *  CSparse         version 3.1.9
- *  CXSparse        version 3.1.8
+ *  CXSparse        version 3.1.9
- *  GPUQREngine     version 1.0.4
+ *  GPUQREngine     version 1.0.5
- *  KLU             version 1.3.7
+ *  KLU             version 1.3.8
- *  LDL             version 2.2.5
+ *  LDL             version 2.2.6
- *  RBio            version 2.2.5
+ *  RBio            version 2.2.6
- *  SPQR            version 2.0.6
+ *  SPQR            version 2.0.8
- *  SuiteSparse_GPURuntime  version 1.0.4
+ *  SuiteSparse_GPURuntime  version 1.0.5
- *  UMFPACK         version 5.7.5
+ *  UMFPACK         version 5.7.6
  *  MATLAB_Tools    various packages & M-files
- *  xerbla          version 1.0.2
+ *  xerbla          version 1.0.3
  *
  * Other package dependencies:
  *  BLAS            required by CHOLMOD and UMFPACK
@@ -211,7 +211,6 @@ int SuiteSparse_divcomplex
  *                  they are compiled with GPU acceleration.
  */
 
-
 int SuiteSparse_version     /* returns SUITESPARSE_VERSION */
 (
     /* output, not defined on input.  Not used if NULL.  Returns
@@ -234,11 +233,11 @@ int SuiteSparse_version     /* returns SUITESPARSE_VERSION */
 */
 #define SUITESPARSE_HAS_VERSION_FUNCTION
 
-#define SUITESPARSE_DATE "Apr 1, 2016"
+#define SUITESPARSE_DATE "Oct 3, 2017"
 #define SUITESPARSE_VER_CODE(main,sub) ((main) * 1000 + (sub))
 #define SUITESPARSE_MAIN_VERSION 4
 #define SUITESPARSE_SUB_VERSION 5
-#define SUITESPARSE_SUBSUB_VERSION 2
+#define SUITESPARSE_SUBSUB_VERSION 6
 #define SUITESPARSE_VERSION \
     SUITESPARSE_VER_CODE(SUITESPARSE_MAIN_VERSION,SUITESPARSE_SUB_VERSION)
 

gtsam/3rdparty/SuiteSparse_config/SuiteSparse_config.mk

@@ -5,7 +5,7 @@
 # This file contains all configuration settings for all packages in SuiteSparse,
 # except for CSparse (which is stand-alone) and the packages in MATLAB_Tools.
 
-SUITESPARSE_VERSION = 4.5.2
+SUITESPARSE_VERSION = 4.5.6
 
 #===============================================================================
 # Options you can change without editing this file:
@@ -115,6 +115,7 @@ SUITESPARSE_VERSION = 4.5.2
             CC = icc -D_GNU_SOURCE
             CXX = $(CC)
             CFOPENMP = -qopenmp -I$(MKLROOT)/include
+	    LDFLAGS += -openmp
         endif
         ifneq ($(shell which ifort 2>/dev/null),)
             # use the Intel ifort compiler for Fortran codes
@@ -123,7 +124,7 @@ SUITESPARSE_VERSION = 4.5.2
     endif
 
     #---------------------------------------------------------------------------
-    # code formatting (for Tcov only)
+    # code formatting (for Tcov on Linux only)
     #---------------------------------------------------------------------------
 
     PRETTY ?= grep -v "^\#" | indent -bl -nce -bli0 -i4 -sob -l120
@@ -224,7 +225,6 @@ SUITESPARSE_VERSION = 4.5.2
         CUDA_INC      = -I$(CUDA_INC_PATH)
         NVCC          = $(CUDA_PATH)/bin/nvcc
         NVCCFLAGS     = -Xcompiler -fPIC -O3 \
-                            -gencode=arch=compute_20,code=sm_20 \
                             -gencode=arch=compute_30,code=sm_30 \
                             -gencode=arch=compute_35,code=sm_35 \
                             -gencode=arch=compute_50,code=sm_50 \
@@ -305,8 +305,9 @@ SUITESPARSE_VERSION = 4.5.2
 
     SPQR_CONFIG ?= $(GPU_CONFIG)
 
-    # to compile with Intel's TBB, use TBB=-ltbb SPQR_CONFIG=-DHAVE_TBB
+    # to compile with Intel's TBB, use TBB=-ltbb -DSPQR_CONFIG=-DHAVE_TBB
     TBB ?=
+    # TBB = -ltbb -DSPQR_CONFIG=-DHAVE_TBB
 
     # TODO: this *mk file should auto-detect the presence of Intel's TBB,
     # and set the compiler flags accordingly.

gtsam/3rdparty/SuiteSparse_config/xerbla/Makefile

@@ -4,7 +4,7 @@
   USE_FORTRAN = 0
 # USE_FORTRAN = 1
 
-VERSION = 1.0.2
+VERSION = 1.0.3
 SO_VERSION = 1
 
 default: library
@@ -35,6 +35,8 @@ ccode: all
 
 fortran: all
 
+static: $(AR_TARGET)
+
 $(AR_TARGET): $(DEPENDS)
 	$(COMPILE)
 	$(ARCHIVE)  $(AR_TARGET) xerbla.o

gtsam/CMakeLists.txt

@@ -25,7 +25,6 @@ add_subdirectory(3rdparty)
 set (3rdparty_srcs
  ${eigen_headers} # Set by 3rdparty/CMakeLists.txt
  ${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/CCOLAMD/Source/ccolamd.c
- ${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/CCOLAMD/Source/ccolamd_global.c
  ${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/SuiteSparse_config/SuiteSparse_config.c)
 gtsam_assign_source_folders("${3rdparty_srcs}") # Create MSVC structure