Eigen

[steersteer]

Hi,
I'm having trouble with pip install of pygalmesh. I get the error "Cannot open include file: 'Eigen/Dense': No such file or directory" could you please give me some guidance on how I can "install" Eigen3 so I can get this to work please?

[nschloe]

You need http://eigen.tuxfamily.org/index.php?title=Main_Page.

On Debian/Ubuntu and derivates, that's as easy as

sudo apt install libeigen3-dev

[steersteer]

Sorry I should have said I'm on a windows machine

[steersteer]

I changed the setup.py line "os.environ.get("EIGEN_INCLUDE_DIR", "\Eigen3")" so I get past that now.
I'm now getting "src/generate.cpp(5): fatal error C1083: Cannot open include file: 'CGAL/Exact_predicates_inexact_constructions_kernel.h': No such file or directory"

As far as I know I have the latest CGAL installed

[nschloe]

These kind of linking errors are nearly impossible to debug without machine access. You'll have to dig around yourself I'm afraid.

[flothesof]

Hi,
I've got a little further down the process trying to install pygalmesh on a Windows machine.

I've done the following:

• install eigen and cgal using conda install -c conda-forge eigen cgal
• added an environment variable 'EIGEN_INCLUDE_DIR' pointing to 'C:\Anaconda3\envs\py37\Library\include\eigen3'

Then doing pip install pygalmesh I'm now stuck on a compile error, which is:

C:\Anaconda3\envs\py37\Library\include\CGAL/Mesh_criteria_3.h(116): error C2664: 'CGAL::Mesh_cell_criteria_3<Tr,CGAL::Mesh_3::Cell_criteria_visitor_with_features<Tr>>::Mesh_cell_criteria_3(const CGAL::Mesh_cell_criteria_3<Tr,CGAL::Mesh_3::Cell_criteria_visitor_with_features<Tr>> &)'ÿ: impossible de convertir l'argument 2 de 'Arg' en 'const double &'
          with
          [
              Tr=pygalmesh::Tr
          ]
          and
          [
              Arg=const pygalmesh::generate_with_sizing_field::<lambda_db8e64dde8d1efacb3178dd659100057>
          ]
  C:\Anaconda3\envs\py37\Library\include\CGAL/Mesh_criteria_3.h(121): note: Raisonÿ: impossible de convertir de 'Arg' en 'const double'
          with
          [
              Arg=const pygalmesh::generate_with_sizing_field::<lambda_db8e64dde8d1efacb3178dd659100057>
          ]

@nschloe Would you be so kind and translate the meaning of that error message for me?

Thank you

Florian

[nschloe]

Looks like an outdated CGAL version.

[flothesof]

Thanks for your quick reply. Indeed, the CGAL version on conda-forge right now is 4.14 (and they're not quite ready to move to CGAL5, see conda-forge/cgal-feedstock#54). So using conda-forge will likely not work until it provides the latest CGAL version... :(

[nschloe]

@flothesof CGAL seems to be updated on conda-forge now. Any interest in writing a recipe for pygalmesh? Would certainly help a number of people.

[flothesof]

Thanks for the suggestion. I've just tried the following on my Mac (not Windows) and it installed pygalmesh successfully:

conda install -c conda-forge eigen cgal
export EIGEN_INCLUDE_DIR=/Users/kappamaki/opt/miniconda3/envs/py37/include/eigen3
git clone https://github.com/nschloe/pygalmesh.git
cd pygalmesh
pip intall -e .

When I run pytest after that, I get:

============================================================================= short test summary info =============================================================================
FAILED test/test_inr.py::test_inr - RuntimeError: Caught an unknown exception!
FAILED test/test_remesh_surface.py::test_inr - meshio._exceptions.ReadError
FAILED test/test_volume_from_surface.py::test_volume_from_surface -   File "<string>", line None
========================================================================== 3 failed, 26 passed in 26.44s ==========================================================================

This may or may not work on Windows, but it seems a good basis for trying to make a recipe on conda-forge. I'll give it a shot (I've never done this before).

[nschloe]

I'm also playing around with it rn. #81

[montallban]

I am on a windows computer. I followed your directions, @flothesof , and got past the Eigen\Dense issue. Now I am hung up on a new one. It seems connected to either my C++ compiler or to CGAL, but I thought CGAL was installed via conda-forge so I don't really know what to do. Any ideas?

Error:

    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.22.27905\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -I\Users\User\usr\include\eigen-3.3.7\ -IC:\Users\User\AppData\Local\Temp\pip-build-env-cva5itsm\normal\Lib\site-packages\pybind11\include -IC:\Users\User\AppData\Local\Temp\pip-build-env-cva5itsm\normal\Lib\site-packages\pybind11\include -IC:\Users\User\Anaconda3\include -IC:\Users\User\Anaconda3\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.22.27905\ATLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.22.27905\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.7.2\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EHsc /Tpsrc/generate.cpp /Fobuild\temp.win-amd64-3.7\Release\src/generate.obj -std=c++14
    cl : Command line warning D9002 : ignoring unknown option '-std=c++14'
    generate.cpp
    src/generate.cpp(5): fatal error C1083: Cannot open include file: 'CGAL/Exact_predicates_inexact_constructions_kernel.h': No such file or directory
    error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\Community\\VC\\Tools\\MSVC\\14.22.27905\\bin\\HostX86\\x64\\cl.exe' failed with exit status 2
    ----------------------------------------
ERROR: Command errored out with exit status 1: 'C:\Users\User\Anaconda3\python.exe' -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\User\\usr\\include\\pygalmesh\\setup.py'"'"'; __file__='"'"'C:\\Users\\User\\usr\\include\\pygalmesh\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.

[nschloe]

@montallban This is a different issue that OP's. Looks like you don't have recent enough version of CGAL installed. Please open a new issue if you need more instructions. https://www.urbandictionary.com/define.php?term=Thread%20Hijacking

[nschloe]

Let me point everyone towards https://anaconda.org/conda-forge/pygalmesh/. This should make installation on Windows a lot easier.