upgrade colamd to suite-sparse-5.4.0
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				|  | @ -1560,9 +1560,8 @@ PUBLIC Int CCOLAMD_2	    /* returns TRUE if successful, FALSE otherwise */ | |||
|     Int *dead_cols ; | ||||
|     Int set1 ; | ||||
|     Int set2 ; | ||||
| #ifndef NDEBUG | ||||
|     Int cs ; | ||||
| #endif | ||||
| 
 | ||||
|     int ok ; | ||||
| 
 | ||||
| #ifndef NDEBUG | ||||
|  | @ -1910,10 +1909,8 @@ PUBLIC Int CCOLAMD_2	    /* returns TRUE if successful, FALSE otherwise */ | |||
|             p [k] = col ; | ||||
|             ASSERT (A [col] == EMPTY) ; | ||||
| 
 | ||||
| #ifndef NDEBUG | ||||
| 	    	cs = CMEMBER (col) ; | ||||
| 	    cs = CMEMBER (col) ; | ||||
|             ASSERT (k >= cset_start [cs] && k < cset_start [cs+1]) ; | ||||
| #endif | ||||
| 
 | ||||
|             A [col] = k ; | ||||
|             k++ ; | ||||
|  | @ -1929,11 +1926,11 @@ PUBLIC Int CCOLAMD_2	    /* returns TRUE if successful, FALSE otherwise */ | |||
|             if (A [col] == EMPTY) | ||||
|             { | ||||
|                 k = Col [col].shared2.order ; | ||||
| 		cs = CMEMBER (col) ; | ||||
| #ifndef NDEBUG | ||||
| 				cs = CMEMBER (col) ; | ||||
|                 dead_cols [cs]-- ; | ||||
|                 ASSERT (k >= cset_start [cs] && k < cset_start [cs+1]) ; | ||||
| #endif | ||||
|                 ASSERT (k >= cset_start [cs] && k < cset_start [cs+1]) ; | ||||
|                 DEBUG1 (("ccolamd output ordering: k "ID" col "ID | ||||
|                     " (dense or null col)\n", k, col)) ; | ||||
|                 p [k] = col ; | ||||
|  |  | |||
|  | @ -7,8 +7,8 @@ export SUITESPARSE | |||
| 
 | ||||
| # version of SuiteSparse_config is also version of SuiteSparse meta-package
 | ||||
| LIBRARY = libsuitesparseconfig | ||||
| VERSION = 4.5.6 | ||||
| SO_VERSION = 4 | ||||
| VERSION = 5.4.0 | ||||
| SO_VERSION = 5 | ||||
| 
 | ||||
| default: library | ||||
| 
 | ||||
|  |  | |||
|  | @ -1,4 +1,4 @@ | |||
| SuiteSparse_config, 2017, Timothy A. Davis, http://www.suitesparse.com | ||||
| SuiteSparse_config, 2018, Timothy A. Davis, http://www.suitesparse.com | ||||
| (formerly the UFconfig package) | ||||
| 
 | ||||
| This directory contains a default SuiteSparse_config.mk file.  It tries to | ||||
|  | @ -37,6 +37,7 @@ SuiteSparse_config is not required by these packages: | |||
| 
 | ||||
|   CSparse       a Concise Sparse matrix package | ||||
|   MATLAB_Tools  toolboxes for use in MATLAB | ||||
|   GraphBLAS     graph algorithms in the language of linear algebra | ||||
| 
 | ||||
| In addition, the xerbla/ directory contains Fortan and C versions of the | ||||
| BLAS/LAPACK xerbla routine, which is called when an invalid input is passed to | ||||
|  |  | |||
|  | @ -4,7 +4,7 @@ | |||
| 
 | ||||
| /* SuiteSparse configuration : memory manager and printf functions. */ | ||||
| 
 | ||||
| /* Copyright (c) 2013, Timothy A. Davis.  No licensing restrictions
 | ||||
| /* Copyright (c) 2013-2018, Timothy A. Davis.  No licensing restrictions
 | ||||
|  * apply to this file or to the SuiteSparse_config directory. | ||||
|  * Author: Timothy A. Davis. | ||||
|  */ | ||||
|  |  | |||
|  | @ -177,38 +177,7 @@ int SuiteSparse_divcomplex | |||
| /* SuiteSparse is not a package itself, but a collection of packages, some of
 | ||||
|  * which must be used together (UMFPACK requires AMD, CHOLMOD requires AMD, | ||||
|  * COLAMD, CAMD, and CCOLAMD, etc).  A version number is provided here for the | ||||
|  * collection itself.  The versions of packages within each version of | ||||
|  * SuiteSparse are meant to work together.  Combining one package from one | ||||
|  * version of SuiteSparse, with another package from another version of | ||||
|  * SuiteSparse, may or may not work. | ||||
|  * | ||||
|  * SuiteSparse contains the following packages: | ||||
|  * | ||||
|  *  SuiteSparse_config version 4.5.6 (version always the same as SuiteSparse) | ||||
|  *  AMD             version 2.4.6 | ||||
|  *  BTF             version 1.2.6 | ||||
|  *  CAMD            version 2.4.6 | ||||
|  *  CCOLAMD         version 2.9.6 | ||||
|  *  CHOLMOD         version 3.0.11 | ||||
|  *  COLAMD          version 2.9.6 | ||||
|  *  CSparse         version 3.1.9 | ||||
|  *  CXSparse        version 3.1.9 | ||||
|  *  GPUQREngine     version 1.0.5 | ||||
|  *  KLU             version 1.3.8 | ||||
|  *  LDL             version 2.2.6 | ||||
|  *  RBio            version 2.2.6 | ||||
|  *  SPQR            version 2.0.8 | ||||
|  *  SuiteSparse_GPURuntime  version 1.0.5 | ||||
|  *  UMFPACK         version 5.7.6 | ||||
|  *  MATLAB_Tools    various packages & M-files | ||||
|  *  xerbla          version 1.0.3 | ||||
|  * | ||||
|  * Other package dependencies: | ||||
|  *  BLAS            required by CHOLMOD and UMFPACK | ||||
|  *  LAPACK          required by CHOLMOD | ||||
|  *  METIS 5.1.0     required by CHOLMOD (optional) and KLU (optional) | ||||
|  *  CUBLAS, CUDART  NVIDIA libraries required by CHOLMOD and SPQR when | ||||
|  *                  they are compiled with GPU acceleration. | ||||
|  * collection itself, which is also the version number of SuiteSparse_config. | ||||
|  */ | ||||
| 
 | ||||
| int SuiteSparse_version     /* returns SUITESPARSE_VERSION */ | ||||
|  | @ -233,11 +202,11 @@ int SuiteSparse_version     /* returns SUITESPARSE_VERSION */ | |||
| */ | ||||
| #define SUITESPARSE_HAS_VERSION_FUNCTION | ||||
| 
 | ||||
| #define SUITESPARSE_DATE "Oct 3, 2017" | ||||
| #define SUITESPARSE_DATE "Dec 28, 2018" | ||||
| #define SUITESPARSE_VER_CODE(main,sub) ((main) * 1000 + (sub)) | ||||
| #define SUITESPARSE_MAIN_VERSION 4 | ||||
| #define SUITESPARSE_SUB_VERSION 5 | ||||
| #define SUITESPARSE_SUBSUB_VERSION 6 | ||||
| #define SUITESPARSE_MAIN_VERSION 5 | ||||
| #define SUITESPARSE_SUB_VERSION 4 | ||||
| #define SUITESPARSE_SUBSUB_VERSION 0 | ||||
| #define SUITESPARSE_VERSION \ | ||||
|     SUITESPARSE_VER_CODE(SUITESPARSE_MAIN_VERSION,SUITESPARSE_SUB_VERSION) | ||||
| 
 | ||||
|  |  | |||
|  | @ -3,9 +3,11 @@ | |||
| #===============================================================================
 | ||||
| 
 | ||||
| # This file contains all configuration settings for all packages in SuiteSparse,
 | ||||
| # except for CSparse (which is stand-alone) and the packages in MATLAB_Tools.
 | ||||
| # except for CSparse (which is stand-alone), the packages in MATLAB_Tools,
 | ||||
| # and GraphBLAS.  The configuration settings for GraphBLAS are determined by
 | ||||
| # GraphBLAS/CMakeLists.txt
 | ||||
| 
 | ||||
| SUITESPARSE_VERSION = 4.5.6 | ||||
| SUITESPARSE_VERSION = 5.4.0 | ||||
| 
 | ||||
| #===============================================================================
 | ||||
| # Options you can change without editing this file:
 | ||||
|  | @ -57,6 +59,15 @@ SUITESPARSE_VERSION = 4.5.6 | |||
|     INSTALL_INCLUDE ?= $(INSTALL)/include | ||||
|     INSTALL_DOC ?= $(INSTALL)/share/doc/suitesparse-$(SUITESPARSE_VERSION) | ||||
| 
 | ||||
|     CMAKE_OPTIONS ?= -DCMAKE_INSTALL_PREFIX=$(INSTALL) | ||||
| 
 | ||||
|     #--------------------------------------------------------------------------- | ||||
|     # parallel make | ||||
|     #--------------------------------------------------------------------------- | ||||
| 
 | ||||
|     # sequential make's by default | ||||
|     JOBS ?= 1 | ||||
| 
 | ||||
|     #--------------------------------------------------------------------------- | ||||
|     # optimization level | ||||
|     #--------------------------------------------------------------------------- | ||||
|  | @ -78,19 +89,11 @@ SUITESPARSE_VERSION = 4.5.6 | |||
|         CXX = g++ | ||||
|         BLAS = -lrefblas -lgfortran -lstdc++ | ||||
|         LAPACK = -llapack | ||||
| 	CFLAGS += --coverage | ||||
| 	OPTIMIZATION = -g | ||||
| 	LDFLAGS += --coverage | ||||
|         CFLAGS += --coverage | ||||
|         OPTIMIZATION = -g | ||||
|         LDFLAGS += --coverage | ||||
|     endif | ||||
| 
 | ||||
|     #--------------------------------------------------------------------------- | ||||
|     # CFLAGS for the C/C++ compiler | ||||
|     #--------------------------------------------------------------------------- | ||||
| 
 | ||||
|     # The CF macro is used by SuiteSparse Makefiles as a combination of | ||||
|     # CFLAGS, CPPFLAGS, TARGET_ARCH, and system-dependent settings. | ||||
|     CF ?= $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) $(OPTIMIZATION) -fexceptions -fPIC | ||||
| 
 | ||||
|     #--------------------------------------------------------------------------- | ||||
|     # OpenMP is used in CHOLMOD | ||||
|     #--------------------------------------------------------------------------- | ||||
|  | @ -112,10 +115,12 @@ SUITESPARSE_VERSION = 4.5.6 | |||
|     ifneq ($(AUTOCC),no) | ||||
|         ifneq ($(shell which icc 2>/dev/null),) | ||||
|             # use the Intel icc compiler for C codes, and -qopenmp for OpenMP | ||||
|             CC = icc -D_GNU_SOURCE | ||||
|             CXX = $(CC) | ||||
|             CC = icc | ||||
|             CFLAGS += -D_GNU_SOURCE | ||||
|             CXX = icpc | ||||
|             CFOPENMP = -qopenmp -I$(MKLROOT)/include | ||||
| 	    LDFLAGS += -openmp | ||||
|             LDFLAGS += -qopenmp | ||||
|             LDLIBS += -lm -lirc | ||||
|         endif | ||||
|         ifneq ($(shell which ifort 2>/dev/null),) | ||||
|             # use the Intel ifort compiler for Fortran codes | ||||
|  | @ -123,6 +128,16 @@ SUITESPARSE_VERSION = 4.5.6 | |||
|         endif | ||||
|     endif | ||||
| 
 | ||||
|     CMAKE_OPTIONS += -DCMAKE_CXX_COMPILER=$(CXX) -DCMAKE_C_COMPILER=$(CC) | ||||
| 
 | ||||
|     #--------------------------------------------------------------------------- | ||||
|     # CFLAGS for the C/C++ compiler | ||||
|     #--------------------------------------------------------------------------- | ||||
| 
 | ||||
|     # The CF macro is used by SuiteSparse Makefiles as a combination of | ||||
|     # CFLAGS, CPPFLAGS, TARGET_ARCH, and system-dependent settings. | ||||
|     CF ?= $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) $(OPTIMIZATION) -fexceptions -fPIC | ||||
| 
 | ||||
|     #--------------------------------------------------------------------------- | ||||
|     # code formatting (for Tcov on Linux only) | ||||
|     #--------------------------------------------------------------------------- | ||||
|  | @ -157,7 +172,7 @@ SUITESPARSE_VERSION = 4.5.6 | |||
|             #   $(MKLROOT)/lib/intel64/libmkl_intel_thread.a \ | ||||
|             #   -Wl,--end-group -lpthread -lm | ||||
|             # using dynamic linking: | ||||
|             BLAS = -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lpthread -lm | ||||
|             BLAS = -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -lpthread -lm | ||||
|             LAPACK = | ||||
|         else | ||||
|             # use the OpenBLAS at http://www.openblas.net | ||||
|  | @ -223,12 +238,16 @@ SUITESPARSE_VERSION = 4.5.6 | |||
|         CUBLAS_LIB    = $(CUDA_PATH)/lib64/libcublas.so | ||||
|         CUDA_INC_PATH = $(CUDA_PATH)/include/ | ||||
|         CUDA_INC      = -I$(CUDA_INC_PATH) | ||||
|                 MAGMA_INC     = -I/opt/magma-2.4.0/include/ | ||||
|                 MAGMA_LIB     = -L/opt/magma-2.4.0/lib/ -lmagma | ||||
|         NVCC          = $(CUDA_PATH)/bin/nvcc | ||||
|         NVCCFLAGS     = -Xcompiler -fPIC -O3 \
 | ||||
|                             -gencode=arch=compute_30,code=sm_30 \
 | ||||
|                             -gencode=arch=compute_35,code=sm_35 \
 | ||||
|                             -gencode=arch=compute_50,code=sm_50 \
 | ||||
|                             -gencode=arch=compute_50,code=compute_50 | ||||
|                             -gencode=arch=compute_53,code=sm_53 \
 | ||||
|                             -gencode=arch=compute_53,code=sm_53 \
 | ||||
|                             -gencode=arch=compute_60,code=compute_60 | ||||
|     endif | ||||
| 
 | ||||
|     #--------------------------------------------------------------------------- | ||||
|  | @ -555,6 +574,7 @@ config: | |||
| 	@echo 'Install include files in: INSTALL_INCLUDE=' '$(INSTALL_INCLUDE)' | ||||
| 	@echo 'Install documentation in: INSTALL_DOC=    ' '$(INSTALL_DOC)' | ||||
| 	@echo 'Optimization level:       OPTIMIZATION=   ' '$(OPTIMIZATION)' | ||||
| 	@echo 'parallel make jobs:       JOBS=           ' '$(JOBS)' | ||||
| 	@echo 'BLAS library:             BLAS=           ' '$(BLAS)' | ||||
| 	@echo 'LAPACK library:           LAPACK=         ' '$(LAPACK)' | ||||
| 	@echo 'Intel TBB library:        TBB=            ' '$(TBB)' | ||||
|  |  | |||
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