CGAL users discussion list

[Daniel Duque <>]

Hi everyone.

Update: I just installed the metis version of suitesparse (libsuitesparse-metis-dev on ubuntu) and now cmake seems to work (I really don't know why). I says:

-- Found CHOLMOD: /usr/include/suitesparse

... but still the compilation fails to find cholmod.h. If I manually change the include line to   "#include <suitesparse/cholmod.h>", compilation works but linking returns lots of errors. I include them, since it seems this is the step that fails.

Thanks,

Daniel

CMakeFiles/main.dir/main.cpp.o: In function `Eigen::CholmodBase<Eigen::SparseMatrix<double, 0, int>, 1, Eigen::CholmodSupern

odalLLT<Eigen::SparseMatrix<double, 0, int>, 1> >::~CholmodBase()':

main.cpp:(.text._ZN5Eigen11CholmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS2_Li1EEEED2Ev[_ZN5Eigen11Cho

lmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS2_Li1EEEED5Ev]+0x19): undefined reference to `cholmod_free

_factor'

main.cpp:(.text._ZN5Eigen11CholmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS2_Li1EEEED2Ev[_ZN5Eigen11Cho

lmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS2_Li1EEEED5Ev]+0x22): undefined reference to `cholmod_fini

sh'

CMakeFiles/main.dir/main.cpp.o: In function `linear::~linear()':

main.cpp:(.text._ZN6linearD2Ev[_ZN6linearD5Ev]+0x25): undefined reference to `cholmod_free_factor'

main.cpp:(.text._ZN6linearD2Ev[_ZN6linearD5Ev]+0x2d): undefined reference to `cholmod_finish'

main.cpp:(.text._ZN6linearD2Ev[_ZN6linearD5Ev]+0x4d): undefined reference to `cholmod_free_factor'

main.cpp:(.text._ZN6linearD2Ev[_ZN6linearD5Ev]+0x55): undefined reference to `cholmod_finish'

main.cpp:(.text._ZN6linearD2Ev[_ZN6linearD5Ev]+0x75): undefined reference to `cholmod_free_factor'

main.cpp:(.text._ZN6linearD2Ev[_ZN6linearD5Ev]+0x7d): undefined reference to `cholmod_finish'

CMakeFiles/main.dir/main.cpp.o: In function `main':

main.cpp:(.text.startup+0x568): undefined reference to `cholmod_start'

main.cpp:(.text.startup+0x5c2): undefined reference to `cholmod_start'

main.cpp:(.text.startup+0x61c): undefined reference to `cholmod_start'

CMakeFiles/main.dir/linear.cpp.o: In function `linear::laplace_div(kind::f, kind::f, kind::f)':

linear.cpp:(.text+0x207c): undefined reference to `cholmod_solve'

linear.cpp:(.text+0x2107): undefined reference to `cholmod_free_dense'

CMakeFiles/main.dir/linear.cpp.o: In function `linear::mass_v(kind::f)':

linear.cpp:(.text+0x2914): undefined reference to `cholmod_solve'

linear.cpp:(.text+0x2968): undefined reference to `cholmod_free_dense'

linear.cpp:(.text+0x2ab8): undefined reference to `cholmod_solve'

linear.cpp:(.text+0x2b0c): undefined reference to `cholmod_free_dense'

CMakeFiles/main.dir/linear.cpp.o: In function `linear::mass_s(kind::f)':

linear.cpp:(.text+0x2f19): undefined reference to `cholmod_solve'

linear.cpp:(.text+0x2f6d): undefined reference to `cholmod_free_dense'

CMakeFiles/main.dir/linear.cpp.o: In function `linear::fill_mas()':

linear.cpp:(.text+0x38fb): undefined reference to `cholmod_free_factor'

linear.cpp:(.text+0x3add): undefined reference to `cholmod_analyze'

linear.cpp:(.text+0x3cee): undefined reference to `cholmod_factorize_p'

CMakeFiles/main.dir/linear.cpp.o: In function `linear::ustar_inv(kind::f, double, kind::f, bool)':

linear.cpp:(.text+0x47e9): undefined reference to `cholmod_solve'

linear.cpp:(.text+0x4860): undefined reference to `cholmod_free_dense'

CMakeFiles/main.dir/linear.cpp.o: In function `Eigen::Matrix<double, -1, 1, 0, -1, 1>::Matrix<Eigen::internal::solve_retval_

base<Eigen::CholmodBase<Eigen::SparseMatrix<double, 0, int>, 1, Eigen::CholmodSupernodalLLT<Eigen::SparseMatrix<double, 0, i

nt>, 1> >, Eigen::Matrix<double, -1, 1, 0, -1, 1> > >(Eigen::ReturnByValue<Eigen::internal::solve_retval_base<Eigen::Cholmod

Base<Eigen::SparseMatrix<double, 0, int>, 1, Eigen::CholmodSupernodalLLT<Eigen::SparseMatrix<double, 0, int>, 1> >, Eigen::M

atrix<double, -1, 1, 0, -1, 1> > > const&)':

linear.cpp:(.text._ZN5Eigen6MatrixIdLin1ELi1ELi0ELin1ELi1EEC2INS_8internal17solve_retval_baseINS_11CholmodBaseINS_12SparseMa

trixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS7_Li1EEEEES1_EEEERKNS_13ReturnByValueIT_EE[_ZN5Eigen6MatrixIdLin1ELi1ELi0ELin1EL

i1EEC5INS_8internal17solve_retval_baseINS_11CholmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS7_Li1EEEEES

1_EEEERKNS_13ReturnByValueIT_EE]+0xbf): undefined reference to `cholmod_solve'

linear.cpp:(.text._ZN5Eigen6MatrixIdLin1ELi1ELi0ELin1ELi1EEC2INS_8internal17solve_retval_baseINS_11CholmodBaseINS_12SparseMa

trixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS7_Li1EEEEES1_EEEERKNS_13ReturnByValueIT_EE[_ZN5Eigen6MatrixIdLin1ELi1ELi0ELin1EL

i1EEC5INS_8internal17solve_retval_baseINS_11CholmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS7_Li1EEEEES

1_EEEERKNS_13ReturnByValueIT_EE]+0x105): undefined reference to `cholmod_free_dense'

CMakeFiles/main.dir/linear.cpp.o: In function `Eigen::CholmodBase<Eigen::SparseMatrix<double, 0, int>, 1, Eigen::CholmodSupe

rnodalLLT<Eigen::SparseMatrix<double, 0, int>, 1> >::analyzePattern(Eigen::SparseMatrix<double, 0, int> const&)':

linear.cpp:(.text._ZN5Eigen11CholmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS2_Li1EEEE14analyzePatternE

RKS2_[_ZN5Eigen11CholmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS2_Li1EEEE14analyzePatternERKS2_]+0x23)

: undefined reference to `cholmod_free_factor'

linear.cpp:(.text._ZN5Eigen11CholmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS2_Li1EEEE14analyzePatternE

RKS2_[_ZN5Eigen11CholmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS2_Li1EEEE14analyzePatternERKS2_]+0x1f5

): undefined reference to `cholmod_analyze'

CMakeFiles/main.dir/linear.cpp.o: In function `Eigen::CholmodBase<Eigen::SparseMatrix<double, 0, int>, 1, Eigen::CholmodSupe

rnodalLLT<Eigen::SparseMatrix<double, 0, int>, 1> >::factorize(Eigen::SparseMatrix<double, 0, int> const&)':

linear.cpp:(.text._ZN5Eigen11CholmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS2_Li1EEEE9factorizeERKS2_[

_ZN5Eigen11CholmodBaseINS_12SparseMatrixIdLi0EiEELi1ENS_20CholmodSupernodalLLTIS2_Li1EEEE9factorizeERKS2_]+0x1e0): undefined

 reference to `cholmod_factorize_p'

collect2: error: ld returned 1 exit status

make[2]: *** [main] Error 1

make[1]: *** [CMakeFiles/main.dir/all] Error 2

make: *** [all] Error 2

On Mon, Nov 2, 2015 at 9:49 AM, Daniel Duque <> wrote:

Hi everyone,

I never understood how cmake works, but up to this day I have been able to hack the CMakeLists.txt file created by the CGAL scripts. I was even able to compile against the Eigen libs even if cmake compiler complained about not finding them. The .h files where found at the compiling step nevertheless.

Right now, I am trying to include the cholmod part of the suitesparse package. In the process, I have learned to include the eigen3 libs, but I am still unable to compile. I include the CMakeLists.txt file below. I run

cmake -DCGAL_DIR=$HOME/CGAL-4.6.3 -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/usr/local/include/eigen-eigen-1306d75b4a21/  .

And I get

-- Build type: Release

-- USING CXXFLAGS = ' -frounding-math -O3 -DNDEBUG'

-- USING EXEFLAGS = '  '

-- Targetting Unix Makefiles

-- Using /usr/bin/c++ compiler.

-- Requested component: Core

-- Requested component: MPFR

-- Requested component: GMP

-- Found Eigen3: /usr/local/include/eigen-eigen-1306d75b4a21/ (found suitable version "3.2.2", minimum required is "3.1.0") 

-- Could NOT find CHOLMOD (missing:  CHOLMOD_LIBRARIES) 

-- Configuring done

-- Generating done

-- Build files have been written to: /home/daniel/fem/embedded

So that when running make I get

-- Build type: Release

-- USING CXXFLAGS = ' -frounding-math -O3 -DNDEBUG'

-- USING EXEFLAGS = '  '

-- Targetting Unix Makefiles

-- Using /usr/bin/c++ compiler.

-- Requested component: Core

-- Requested component: MPFR

-- Requested component: GMP

-- Configuring done

-- Generating done

-- Build files have been written to: /home/daniel/fem/embedded

Scanning dependencies of target main

[  9%] Building CXX object CMakeFiles/main.dir/main.cpp.o

In file included from /home/daniel/fem/embedded/linear.h:4:0,

                 from /home/daniel/fem/embedded/main.cpp:11:

/usr/local/include/eigen-eigen-1306d75b4a21/Eigen/CholmodSupport:9:23: fatal error: cholmod.h: No such file or directory

   #include <cholmod.h>

                       ^

compilation terminated.

make[2]: *** [CMakeFiles/main.dir/main.cpp.o] Error 1

make[1]: *** [CMakeFiles/main.dir/all] Error 2

make: *** [all] Error 2

The cholmod.h file is at /use/include/suitesparse, so that changing that line to #include <suitesparse/cholmod.h> leads to a successful compilation... but then linking fails.

I realize this is really not a CGAL topic, but I am sure there are people here who know about cmake.

Thanks very much in advance,

Daniel

The file:

# Created by the script cgal_create_cmake_script

# This is the CMake script for compiling a CGAL application.

project( embedded_ )

cmake_minimum_required(VERSION 2.6.2)

if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" VERSION_GREATER 2.6)

  if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.${CMAKE_PATCH_VERSION}" VERSION_GREATER 2.8.3)

    cmake_policy(VERSION 2.8.4)

  else()

    cmake_policy(VERSION 2.6)

  endif()

endif()

# These don't work ...

#set(CGAL_DIR "${HOME}/CGAL-4.6.3")

#set(CMAKE_BUILD_TYPE "Release")

find_package(CGAL QUIET COMPONENTS Core )

include( ${CGAL_USE_FILE} )

set(EIGEN3_INCLUDE_DIR "/usr/local/include/eigen-eigen-1306d75b4a21/")

find_package(Eigen3)

if(EIGEN3_FOUND)

   include( ${EIGEN3_USE_FILE} )

else()

   message(STATUS "NOTICE: Eigen library is not found.")

endif()

set(CMAKE_MODULE_PATH "/usr/local/include/eigen-eigen-1306d75b4a21/cmake;${CMAKE_MODULE_PATH}")

set(CHOLMOD_LIBRARIES "/usr/include/suitesparse/")

find_package( Cholmod )

include( CGAL_CreateSingleSourceCGALProgram )

create_single_source_cgal_program("main.cpp" "linear.cpp"   "gradient.cpp"  "nabla.cpp" "quad_coeffs.cpp" "periodic.cpp" "fi

elds.cpp" "Delta.cpp" "move.cpp" "draw.cpp" "onto_from_mesh.cpp" )