cmake configure does not find cgal

[Praveen C]

Hello 

I have cgal installed via spack

$ spack location -i cgal
/home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy

and I add

-DDEAL_II_CXX_FLAGS="-march=native -std=c++17" \

-DCGAL_DIR=`spack location -i cgal`  \

-DDEAL_II_WITH_CGAL:BOOL=ON  \

but cmake cannot find it. Any ideas what could be wrong ?

Thanks

praveen

---------------------------------------------

-- Include /home/praveen/Applications/deal.II/9.5.1/cmake/configure/configure_50_cgal.cmake

-- Processing CGAL variables and targets

--   CGAL_INCLUDE_DIRS: *** Required variable "CGAL_INCLUDE_DIRS" empty ***

-- Unable to process CGAL

-- DEAL_II_WITH_CGAL has unmet external dependencies.

CMake Error at cmake/macros/macro_configure_feature.cmake:112 (message):

  

  Could not find the cgal library!

  Please ensure that a suitable cgal library is installed on your computer.

  If the library is not at a default location, either provide some hints for

  autodetection,

      $ CGAL_DIR="..." cmake <...>

      $ cmake -DCGAL_DIR="..." <...>

  or set the relevant variables by hand in ccmake.

Call Stack (most recent call first):

  cmake/macros/macro_configure_feature.cmake:277 (feature_error_message)

  cmake/configure/configure_50_cgal.cmake:80 (configure_feature)

  cmake/macros/macro_verbose_include.cmake:19 (include)

  CMakeLists.txt:120 (verbose_include)

[Wolfgang Bangerth]

On 1/4/24 08:40, Praveen C wrote:
>
> -DDEAL_II_CXX_FLAGS="-march=native -std=c++17"\
>
> -DCGAL_DIR=`spack location -i cgal`\
>
> -DDEAL_II_WITH_CGAL:BOOL=ON \
>
>
> but cmake cannot find it. Any ideas what could be wrong ?

What does
spack location -i cgal
return? And are the files that cmake looks for in that directory? To see which
files cmake will look for, check cmake/configure/configure_50_cgal.cmake.

Best
W.

--
------------------------------------------------------------------------
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www: http://www.math.colostate.edu/~bangerth/

[timo Hyvärinen]

hi, paraveen

I think -DCGAL_DIR="/home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy" will be better if spack location -i cgal return the library dictionary i.e., it contains include/, lib/.

I'm not sure if shell evaluation (`` or $()) would be directly assigned to cmake variables in the way you posted.

best,

timo

"

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[Praveen C]

spack location -i cgal

/home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy

does return the correct directory, which contains

CGAL/include, etc., and they do have the include files.

I have tried directly putting the cgal directory path also, it does not help. My configure script which is below, works fine in finding all directories, except cgal.

Thanks

praveen

`spack location -i cmake`/bin/cmake  \

-DCMAKE_INSTALL_PREFIX=$DEAL_II_DIR \

-DCMAKE_FIND_FRAMEWORK=LAST  \

-DCMAKE_BUILD_TYPE=DebugRelease  \

-DDEAL_II_COMPONENT_EXAMPLES=ON  \

-DDEAL_II_COMPILE_EXAMPLES=OFF \

-DDEAL_II_WITH_LAPACK=ON \

-DLAPACK_INCLUDE_DIRS=`spack location -i openblas`/include  \

-DLAPACK_LIBRARIES=`spack location -i openblas`/lib/${LAPACK_LIBRARY}  \

-DBOOST_DIR=`spack location -i boost`  \

-DDEAL_II_WITH_ARBORX=ON \

-DARBORX_DIR=`spack location -i arborx`  \

-DMUPARSER_DIR=`spack location -i muparser`  \

-DUMFPACK_DIR=`spack location -i suite-sparse`  \

-DTBB_DIR=`spack location -i intel-tbb`  \

-DZLIB_DIR=`spack location -i zlib-ng`  \

-DDEAL_II_WITH_MPI:BOOL=ON  \

-DCMAKE_C_COMPILER=$MPI_DIR/bin/mpicc  \

-DCMAKE_CXX_COMPILER=$MPI_DIR/bin/mpic++  \

-DCMAKE_Fortran_COMPILER=$MPI_DIR/bin/mpif90  \

-DDEAL_II_CXX_FLAGS="-march=native -mtune=native -std=c++17" \

-DDEAL_II_CXX_FLAGS_RELEASE="-O3" \

-DGSL_DIR=`spack location -i gsl`  \

-DDEAL_II_WITH_GSL:BOOL=ON  \

-DCGAL_DIR=`spack location -i cgal`  \

-DDEAL_II_WITH_CGAL:BOOL=ON  \

-DHDF5_DIR=`spack location -i hdf5`  \

-DDEAL_II_WITH_HDF5:BOOL=ON  \

-DP4EST_DIR=`spack location -i p4est`  \

-DDEAL_II_WITH_P4EST:BOOL=ON  \

-DPETSC_DIR=`spack location -i petsc`  \

-DDEAL_II_WITH_PETSC:BOOL=ON  \

-DSLEPC_DIR=`spack location -i slepc`  \

-DDEAL_II_WITH_SLEPC:BOOL=ON  \

-DTRILINOS_DIR=`spack location -i trilinos`  \

-DDEAL_II_WITH_TRILINOS:BOOL=ON  \

-DMETIS_DIR=`spack location -i metis`  \

-DDEAL_II_WITH_METIS:BOOL=ON  \

-DDEAL_II_COMPONENT_DOCUMENTATION=OFF  \

-DARPACK_DIR=`spack location -i arpack-ng`  \

-DDEAL_II_WITH_ARPACK=ON  \

-DDEAL_II_ARPACK_WITH_PARPACK=ON  \

-DOPENCASCADE_DIR=`spack location -i oce`  \

-DDEAL_II_WITH_OPENCASCADE=ON  \

-DGMSH_DIR=$GMSH_DIR \

-DDEAL_II_WITH_GMSH=$DEAL_II_WITH_GMSH  \

-DASSIMP_DIR=`spack location -i assimp`  \

-DDEAL_II_WITH_ASSIMP=ON  \

-DSUNDIALS_DIR=`spack location -i sundials`  \

-DDEAL_II_WITH_SUNDIALS=ON  \

-DADOLC_DIR=`spack location -i adol-c`  \

-DDEAL_II_WITH_ADOLC=ON  \

-DSCALAPACK_DIR=`spack location -i netlib-scalapack`  \

-DDEAL_II_WITH_SCALAPACK=ON  \

-DDEAL_II_WITH_GINKGO=ON  \

-DGINKGO_DIR=`spack location -i ginkgo`  \

-DDEAL_II_WITH_SYMENGINE=ON  \

-DSYMENGINE_DIR=`spack location -i symengine`  \

../

[Luca Heltai]

Can you post the detailed.log file?

Luca

Il giorno 5 gen 2024, alle ore 03:48, Praveen C <pra...@math.tifrbng.res.in> ha scritto:

spack location -i cgal

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[Praveen C]

Hello Luca

Since cmake configure fails, at that stage no detailed.log is present, and I did not find any other log file in the build directory.

Thanks

praveen

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[Praveen C]

In cmake/modules/FindDEAL_II_CGAL.cmake

I print CGAL_DIR and remove QUIET

#

# CGAL requires C++17 and an externally configured Boost, otherwise the

# call to find_package(CGAL) will fail. Guard the call to FIND_PACKAGE to

# fail gracefully:

#

if(DEAL_II_HAVE_CXX17 AND NOT DEAL_II_FEATURE_BOOST_BUNDLED_CONFIGURED)

  set(CGAL_DO_NOT_WARN_ABOUT_CMAKE_BUILD_TYPE ON)

  #find_package(CGAL QUIET)

  message(STATUS ${CGAL_DIR})

  find_package(CGAL)

It prints CGAL_DIR correctly but shows some warnings and then error

-- Include /home/praveen/Applications/deal.II/9.5.1/cmake/configure/configure_50_cgal.cmake

-- /home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy <=== CGAL_DIR

CMake Warning at cmake/modules/FindDEAL_II_CGAL.cmake:43 (find_package):

  By not providing "FindCGAL.cmake" in CMAKE_MODULE_PATH this project has

  asked CMake to find a package configuration file provided by "CGAL", but

  CMake did not find one.

  Could not find a package configuration file provided by "CGAL" with any of

  the following names:

    CGALConfig.cmake

    cgal-config.cmake

  Add the installation prefix of "CGAL" to CMAKE_PREFIX_PATH or set

  "CGAL_DIR" to a directory containing one of the above files.  If "CGAL"

  provides a separate development package or SDK, be sure it has been

  installed.

Call Stack (most recent call first):

  cmake/configure/configure_50_cgal.cmake:31 (find_package)

  build/CMakeFiles/CMakeTmp/evaluate_expression.tmp:1 (feature_CGAL_find_external)

  cmake/macros/macro_evaluate_expression.cmake:30 (include)

  cmake/macros/macro_configure_feature.cmake:239 (evaluate_expression)

  cmake/configure/configure_50_cgal.cmake:80 (configure_feature)

  cmake/macros/macro_verbose_include.cmake:19 (include)

  CMakeLists.txt:120 (verbose_include)

-- Processing CGAL variables and targets

--   CGAL_INCLUDE_DIRS: *** Required variable "CGAL_INCLUDE_DIRS" empty ***

-- Unable to process CGAL

-- DEAL_II_WITH_CGAL has unmet external dependencies.

CMake Error at cmake/macros/macro_configure_feature.cmake:112 (message):

  

  Could not find the cgal library!

  Please ensure that a suitable cgal library is installed on your computer.

  If the library is not at a default location, either provide some hints for

  autodetection,

      $ CGAL_DIR="..." cmake <...>

      $ cmake -DCGAL_DIR="..." <...>

  or set the relevant variables by hand in ccmake.

Call Stack (most recent call first):

  cmake/macros/macro_configure_feature.cmake:277 (feature_error_message)

  cmake/configure/configure_50_cgal.cmake:80 (configure_feature)

  cmake/macros/macro_verbose_include.cmake:19 (include)

  CMakeLists.txt:120 (verbose_include)

I do see the file CGALConfig.cmake inside CGAL_DIR

$ pwd

/Users/praveen/Applications/spack/opt/spack/darwin-sonoma-m1/apple-clang-15.0.0/cgal-5.5.2-zkfj3cdu7rx32vkhs76cwdp2ivzu7l7z

--------------------------------------------------------------------------------$ find . -name CGALConfig.cmake

./lib/cmake/CGAL/CGALConfig.cmake

Does any of this shed some light on the issue ?

Thanks

praveen

[timo Hyvärinen]

hi, praveen

Did you check which Boost deal.ii was built from? The external one or bundled one? If deal.ii didn't detect what "DBOOST_DIR=`spack location -i boost` " is provided, then bundled Boost will be built.

If this happens, according to " CGAL requires C++17 and an externally configured Boost, otherwise the call to find_package(CGAL) will fail.", cagl will missing.

Best,

tim

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[Praveen C]

Boost is external, from spack. That works fine, I can compile deal.II with this external boost if I disable cgal.

Thanks

praveen

[timo Hyvärinen]

hi, praveen

Is this error reproducible on a non-spack packaging system? A minimal test could be building deal.ii with manually complied cgal.

best,

tim

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[Praveen C]

Hello Tim

I download cgal-5.6 and use that, it seems there is no need to compile it as it is include only.

And cmake does succeed to configure, I had to add

-DGMP_INCLUDE_DIR=`spack location -i gmp` \

-DGMP_LIBRARIES=`spack location -i gmp` \

-DMPFR_INCLUDE_DIR=`spack location -i mpfr` \

-DMPFR_LIBRARIES=`spack location -i mpfr` \

I get many warnings about gmp and mpfr

###

-- Configuring done (36.5s)

CMake Warning at cmake/macros/macro_define_interface_target.cmake:108 (target_link_libraries):

  Target "dealii_debug" requests linking to directory

  "/home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/mpfr-4.2.0-7ooamwzcp4niksyhxurjgww5m4odfbxz".

  Targets may link only to libraries.  CMake is dropping the item.

Call Stack (most recent call first):

  cmake/macros/macro_configure_feature.cmake:251 (define_interface_target)

  cmake/configure/configure_50_cgal.cmake:80 (configure_feature)

  cmake/macros/macro_verbose_include.cmake:19 (include)

  CMakeLists.txt:120 (verbose_include)

CMake Warning at cmake/macros/macro_define_interface_target.cmake:108 (target_link_libraries):

  Target "dealii_debug" requests linking to directory

  "/home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/gmp-6.2.1-wiruostcmgopt2jwillj24wkz3healpd".

  Targets may link only to libraries.  CMake is dropping the item.

Call Stack (most recent call first):

  cmake/macros/macro_configure_feature.cmake:251 (define_interface_target)

  cmake/configure/configure_50_cgal.cmake:80 (configure_feature)

  cmake/macros/macro_verbose_include.cmake:19 (include)

  CMakeLists.txt:120 (verbose_include)

CMake Warning at cmake/macros/macro_define_interface_target.cmake:108 (target_link_libraries):

  Target "dealii_release" requests linking to directory

  "/home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/mpfr-4.2.0-7ooamwzcp4niksyhxurjgww5m4odfbxz".

  Targets may link only to libraries.  CMake is dropping the item.

Call Stack (most recent call first):

  cmake/macros/macro_configure_feature.cmake:251 (define_interface_target)

  cmake/configure/configure_50_cgal.cmake:80 (configure_feature)

  cmake/macros/macro_verbose_include.cmake:19 (include)

  CMakeLists.txt:120 (verbose_include)

CMake Warning at cmake/macros/macro_define_interface_target.cmake:108 (target_link_libraries):

  Target "dealii_release" requests linking to directory

  "/home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/gmp-6.2.1-wiruostcmgopt2jwillj24wkz3healpd".

  Targets may link only to libraries.  CMake is dropping the item.

Call Stack (most recent call first):

  cmake/macros/macro_configure_feature.cmake:251 (define_interface_target)

  cmake/configure/configure_50_cgal.cmake:80 (configure_feature)

  cmake/macros/macro_verbose_include.cmake:19 (include)

  CMakeLists.txt:120 (verbose_include)

So there does seem to be some issue with cgal installation via spack.

I could compile deal.II but running step-1 gives this

###

-- Configuring done (1.8s)

CMake Warning at /home/praveen/Applications/deal.II/9.5.1/install/lib/cmake/deal.II/deal.IITargets.cmake:191 (set_target_properties):

  Target "step-1" requests linking to directory

  "/home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/mpfr-4.2.0-7ooamwzcp4niksyhxurjgww5m4odfbxz".

  Targets may link only to libraries.  CMake is dropping the item.

Call Stack (most recent call first):

  /home/praveen/Applications/deal.II/9.5.1/install/share/deal.II/macros/macro_deal_ii_setup_target.cmake:52 (include)

  /home/praveen/Applications/deal.II/9.5.1/install/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake:76 (deal_ii_setup_target)

  CMakeLists.txt:39 (deal_ii_invoke_autopilot)

CMake Warning at /home/praveen/Applications/deal.II/9.5.1/install/lib/cmake/deal.II/deal.IITargets.cmake:191 (set_target_properties):

  Target "step-1" requests linking to directory

  "/home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/gmp-6.2.1-wiruostcmgopt2jwillj24wkz3healpd".

  Targets may link only to libraries.  CMake is dropping the item.

Call Stack (most recent call first):

  /home/praveen/Applications/deal.II/9.5.1/install/share/deal.II/macros/macro_deal_ii_setup_target.cmake:52 (include)

  /home/praveen/Applications/deal.II/9.5.1/install/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake:76 (deal_ii_setup_target)

  CMakeLists.txt:39 (deal_ii_invoke_autopilot)

-- Generating done (0.1s)

-- Build files have been written to: /home/praveen/Applications/deal.II/9.5.1/examples/step-1

$ make

[ 50%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o

[100%] Linking CXX executable step-1

[100%] Built target step-1

$ ./step-1

step-1: malloc.c:2382: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.

Aborted (core dumped)

I have to try compiling without cgal and see what happens.

Thanks

praveen

On 05-Jan-2024, at 5:33 PM, timo Hyvärinen <hyvarin...@gmail.com> wrote:

hi, praveen

[Praveen C]

So this error

On 05-Jan-2024, at 7:28 PM, Praveen C <cpra...@gmail.com> wrote:

[100%] Built target step-1

$ ./step-1

step-1: malloc.c:2382: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.

Aborted (core dumped)

happens even if I compile dealii without cgal.

I upgraded os/compilers few days back.

Thanks

praveen

[timo Hyvärinen]

hi, praveen

I think spack did cause something went wrong, building deal.ii with cgal without spack may be a good way.

bset,

Tim  

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[Daniel Arndt]

It seems like the spark installation doesn't provide FindCGAL.cmake or at least not in the path that you provide as CGAL_DIR.

Can you try finding that file and (if it exists) setting the respective directory as CGAL_DIR?

Best,

Daniel

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[Praveen C]

I think deal.II is supposed to provide FindCGAL.cmake, there is no such file inside cgal.

Thanks

praveen

[Daniel Arndt]

What about CGALConfig.cmake? A CMake project installation should provide that.

Best,

Daniel

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[Praveen C]

CGALConfig.cmake is present

$ ls -l `spack location -i cgal`/lib64/cmake/CGAL/CGALConfig*
-rw-r--r-- 1 praveen 8.5K Jun 13  2022 /home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy/lib64/cmake/CGAL/CGALConfig_binary.cmake.in
-rw-r--r-- 1 praveen  144 Jun 13  2022 /home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy/lib64/cmake/CGAL/CGALConfig_binary_header_only.cmake.in
-rw-r--r-- 1 praveen   28 Feb 25  2023 /home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy/lib64/cmake/CGAL/CGALConfigBuildVersion.cmake
-rw-r--r-- 1 praveen 6.3K Nov 26  2022 /home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy/lib64/cmake/CGAL/CGALConfig.cmake
-rw-r--r-- 1 praveen 8.4K Jun 13  2022 /home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy/lib64/cmake/CGAL/CGALConfig_install.cmake.in
-rw-r--r-- 1 praveen  158 Jun 13  2022 /home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy/lib64/cmake/CGAL/CGALConfigVersion_binary_header_only.cmake.in
-rw-r--r-- 1 praveen  951 Oct 15  2022 /home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy/lib64/cmake/CGAL/CGALConfigVersion.cmake

Thanks

praveen

[Daniel Arndt]

What happens if you configure with CGAL_DIR= /home/spack/opt/spack/linux-opensuse15-broadwell/gcc-12.3.0/cgal-5.5.2-6umjskepmayihkexoscjiovjmtgo5toy/lib64/cmake/CGAL ?

Best,

Daniel

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