Issue linking GMSH when installing & building dealii 9.4

[Matthew Rich]

Hi all, 

I was upgrading the 9.4 and I needed to include GMSH for a project I am working on so I can use the API in my dealii code. I am getting the following error despite getting the all clear from CMAKE. How can I fix this , are there version limits on GMSH? I did notice this line "netgen, tetgen and blas support has to be enabled in Gmsh"  How does one ensure that? I do not see much in their github readme. 

Some details- 

On a windows system running dealii in WSL2 under debian. I have built gmsh from source and it is functional by itself, so I feel I did that part right.  I have -DGMSH_DIR set to the root directory of my gmsh installation so ~/gmsh-gmsh-4.10.5 cmake settings when I install dealii  

make Error 

[ 75%] Linking CXX executable ../bin/step_3_mixed.debug
../lib/libdeal_II.g.so.9.4.0: error: undefined reference to 'gmsh::model::addPhysicalGroup(int, std::vector<int, std::allocator<int> > const&, int)'
../lib/libdeal_II.g.so.9.4.0: error: undefined reference to 'gmsh::model::mesh::removeDuplicateNodes()'
../lib/libdeal_II.g.so.9.4.0: error: undefined reference to 'gmsh::initialize(int, char**, bool)'
collect2: error: ld returned 1 exit status
make[2]: *** [examples/CMakeFiles/step_3_mixed.debug.dir/build.make:292: bin/step_3_mixed.debug] Error 1
make[1]: *** [CMakeFiles/Makefile2:3926: examples/CMakeFiles/step_3_mixed.debug.dir/all] Error 2
make: *** [Makefile:149: all] Error 2

CMAKE output 

#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION = ON):
#      ( DEAL_II_WITH_64BIT_INDICES = OFF )
#      ( DEAL_II_WITH_ADOLC = OFF )
#      ( DEAL_II_WITH_ARBORX = OFF )
#        DEAL_II_WITH_ARPACK set up with external dependencies
#        DEAL_II_WITH_ASSIMP set up with external dependencies
#        DEAL_II_WITH_BOOST set up with external dependencies
#      ( DEAL_II_WITH_CGAL = OFF )
#        DEAL_II_WITH_COMPLEX_VALUES = ON
#      ( DEAL_II_WITH_CUDA = OFF )
#      ( DEAL_II_WITH_GINKGO = OFF )
#        DEAL_II_WITH_GMSH set up with external dependencies
#        DEAL_II_WITH_GSL set up with external dependencies
#        DEAL_II_WITH_HDF5 set up with external dependencies
#        DEAL_II_WITH_KOKKOS set up with external dependencies
#        DEAL_II_WITH_LAPACK set up with external dependencies
#        DEAL_II_WITH_METIS set up with external dependencies
#        DEAL_II_WITH_MPI set up with external dependencies
#        DEAL_II_WITH_MUPARSER set up with external dependencies
#        DEAL_II_WITH_OPENCASCADE set up with external dependencies
#        DEAL_II_WITH_P4EST set up with external dependencies
#        DEAL_II_WITH_PETSC set up with external dependencies
#        DEAL_II_WITH_SCALAPACK set up with external dependencies
#        DEAL_II_WITH_SLEPC set up with external dependencies
#      ( DEAL_II_WITH_SUNDIALS = OFF )
#      ( DEAL_II_WITH_SYMENGINE = OFF )
#        DEAL_II_WITH_TBB set up with external dependencies
#        DEAL_II_WITH_TRILINOS set up with external dependencies
#        DEAL_II_WITH_UMFPACK set up with external dependencies
#        DEAL_II_WITH_ZLIB set up with external dependencies
#
#  Component configuration:
#      ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
#        DEAL_II_COMPONENT_EXAMPLES
#      ( DEAL_II_COMPONENT_PACKAGE = OFF )
#      ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
#  Detailed information (compiler flags, feature configuration) can be found in detailed.log
#
#  Run  $ make info  to print a help message with a list of top level targets
#
###
-- Configuring done
-- Generating done
-- Build files have been written to: /home/mjrich/dealii-9.4.0/build

[Daniel Arndt]

Matthew,

I don't know if the missing references are due to missing components in your gmsh installation (but I wouldn't be surprised).

In any way, "netgen, tetgen and blas support has to be enabled in Gmsh" relates to CMake options when building gmsh from source, e.g., https://gmsh.info/src/gmsh-4.10.5-source.tgz.

I would try if building gmsh yourself with those dependencies/options resolves the issue.

Best,

Daniel

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[Matthew Rich]

Thanks for the reply.  I tried building from source a couple times and no luck. I see tetgen and netgen in the cmake output but not  blas

Anyone do this recently? I have LAPACK debian package but that does not seem to do the job. I think this is my issue is BLAS is missing but not sure how to rectify. 

cmake output  for GMSH

cmake -DENABLE_BUILD_DYNAMIC=1 -DENABLE_BUILD_SHARED=1 -DENABLE_MUMPS=1 -ENABLE_NUMPY=1 -DENABLE_PETSC4PY=1 -DENABLE_OCC_TBB=1 -DENABLE_OPENACC=1 -DENABLE_PETSC=1 -DENABLE_REVOROPT=1 -VERBOSE=1 ../
-- Found 64Bit
-- Found OpenMP
-- Found OpenACC_C: -fopenacc
-- Found OpenACC_CXX: -fopenacc
-- Found OpenACC
-- Found Eigen[contrib]
-- Found Mesh
-- Found Solver
-- Found Post
-- Found Plugins
-- Found Parser
CMake Warning (dev) at /usr/share/cmake-3.18/Modules/FindOpenGL.cmake:305 (message):
  Policy CMP0072 is not set: FindOpenGL prefers GLVND by default when
  available.  Run "cmake --help-policy CMP0072" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  FindOpenGL found both a legacy GL library:

    OPENGL_gl_LIBRARY: /usr/lib/x86_64-linux-gnu/libGL.so

  and GLVND libraries for OpenGL and GLX:

    OPENGL_opengl_LIBRARY: /usr/lib/x86_64-linux-gnu/libOpenGL.so
    OPENGL_glx_LIBRARY: /usr/lib/x86_64-linux-gnu/libGLX.so

  OpenGL_GL_PREFERENCE has not been set to "GLVND" or "LEGACY", so for
  compatibility with CMake 3.10 and below the legacy GL library will be used.
Call Stack (most recent call first):
  /usr/share/cmake-3.18/Modules/FindFLTK.cmake:83 (find_package)
  CMakeLists.txt:633 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Could NOT find FLTK (missing: FLTK_LIBRARIES)
-- Found ONELAB
-- Found ONELABMetamodel
-- Found ANN[contrib]
-- Found ALGLIB[contrib]
-- Found DIntegration
-- Found Kbipack
-- GMP not found: Kbipack uses long int
-- Found MathEx[contrib]
-- Found Metis[contrib]
-- Found TetGen/BR
-- Found Voro++[contrib]
-- Found OptHom
-- Found DomHex
-- Found QuadTri
-- Found Blossom
-- Found Netgen
-- Found Bamg
-- Found Hxt
-- Found QuadMeshingTools
-- Found WinslowUntangler
-- Found Gmm[contrib]
-- Found PETSc
-- Found OpenCASCADE version 7.5.1 in /usr/include/opencascade
-- Found OpenCASCADE-CAF
-- Found OpenCASCADE
-- Found Dlopen
-- Found LinuxJoystick
-- Found Revoropt
--
-- Gmsh 4.10.5 has been configured for Linux64-sdk
--
--  * Build options: 64Bit ALGLIB[contrib] ANN[contrib] Bamg Blossom DIntegration Dlopen DomHex Eigen[contrib] Gmm[contrib] Hxt Kbipack LinuxJoystick MathEx[contrib] Mesh Metis[contrib] Netgen ONELAB ONELABMetamodel OpenACC OpenCASCADE OpenCASCADE-CAF OpenMP OptHom PETSc Parser Plugins Post QuadMeshingTools QuadTri Revoropt Solver TetGen/BR Voro++[contrib] WinslowUntangler
--  * Build type: RelWithDebInfo
--  * C compiler: /usr/bin/cc
--  * C++ compiler: /usr/bin/c++
--  * Install prefix: /usr/local
--

-- Configuring done
-- Generating done

-- Build files have been written to: /home/mjrich/gmsh-4.10.5

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