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astrojuanlu / fenics-recipes

This repository contains conda recipes for the FEniCS libraries
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VTK version is too recent #33

Closed e-aranda closed 8 years ago

e-aranda commented 8 years ago

Hi,

I have installed fenics following instructions from "Binary installation using conda" and importing dolfin gives me the following error: ImportError: libvtkWidgets.so.5.10: cannot open shared object file: No such file or directory

Any hints?

Thanks, Ernesto

astrojuanlu commented 8 years ago

Hi Ernesto, could you check if VTK is installed?

$ conda list vtk

Otherwise you will have to install it. If it is not installed it's strange because it's listed as a requirement of DOLFIN, and if it is installed then I will have to investigate why the library is not found.

e-aranda commented 8 years ago

Yes, $ conda list vtk gives

# packages in environment at /home/earanda/anaconda:
#
vtk                       6.3.0                    py27_0

There many libvtk* files in anaconda/envs/fenics27/lib but libvtkWidgets* is missing.

e-aranda commented 8 years ago

Sorry, I meant in anaconda/lib there many libvtk* files.

astrojuanlu commented 8 years ago

Make sure which environment are you using (the root one or fenics27). Anyway it seems likely that I did not put a constraint on the VTK version and the one that got installed is too recent. Try this:

$ conda install "vtk=5.10"

So I will have to update the packages to avoid this.

e-aranda commented 8 years ago

I have downgraded the vtk version, but the result is the same, but now, libvtkWidgets is there !!!

Look:

$ which python
/home/earanda/anaconda/envs/fenics27/bin/python`
$ locate libvtkWidgets
/home/earanda/anaconda/lib/libvtkWidgets.so
/home/earanda/anaconda/lib/libvtkWidgets.so.5.10
/home/earanda/anaconda/lib/libvtkWidgets.so.5.10.1
/home/earanda/anaconda/lib/libvtkWidgetsPythonD.so
/home/earanda/anaconda/lib/libvtkWidgetsPythonD.so.5.10
/home/earanda/anaconda/lib/libvtkWidgetsPythonD.so.5.10.1
/home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgets.so
/home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgets.so.5.10
/home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgets.so.5.10.1
/home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgetsPythonD.so
/home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgetsPythonD.so.5.10
/home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgetsPythonD.so.5.10.1

Now, I understand nothing!

astrojuanlu commented 8 years ago

I think you installed VTK in the root environment, but FEniCS in fenics27! Can you try these commands?

$ source activate fenics27 (fenics27) $ conda list On Oct 9, 2015 11:32 AM, "e-aranda" notifications@github.com wrote:

I have downgraded the vtk version, but the result is the same, but now, libvtkWidgets is there !!!

Look:

earanda@eranda-desktop:~$ which python /home/earanda/anaconda/envs/fenics27/bin/python earanda@eranda-desktop:~$ locate libvtkWidgets /home/earanda/anaconda/lib/libvtkWidgets.so /home/earanda/anaconda/lib/libvtkWidgets.so.5.10 /home/earanda/anaconda/lib/libvtkWidgets.so.5.10.1 /home/earanda/anaconda/lib/libvtkWidgetsPythonD.so /home/earanda/anaconda/lib/libvtkWidgetsPythonD.so.5.10 /home/earanda/anaconda/lib/libvtkWidgetsPythonD.so.5.10.1 /home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgets.so /home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgets.so.5.10 /home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgets.so.5.10.1 /home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgetsPythonD.so

/home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgetsPythonD.so.5.10

/home/earanda/anaconda/pkgs/vtk-5.10.1-py27_1/lib/libvtkWidgetsPythonD.so.5.10.1

Now, I understand nothing!

— Reply to this email directly or view it on GitHub https://github.com/Juanlu001/fenics-recipes/issues/33#issuecomment-146812130 .

e-aranda commented 8 years ago

Yes, you are right! Here, vtk is in 6.3.0 version. I don't know how conda works? How can I do?

 $ source activate fenics27
 discarding /home/earanda/anaconda/bin from PATH
 prepending /home/earanda/anaconda/envs/fenics27/bin to PATH
 (fenics27)earanda@eranda-desktop:~$ conda list
 # packages in environment at /home/earanda/anaconda/envs/fenics27:
 #
 boost                     1.57.0                        4  
 cmake                     3.2.3                         0  
 dolfin                    1.6.0                    py27_2  
 eigen3                    3.2.1                         1   
 fastcache                 1.0.2                    py27_0  
 fenics                    1.6.0                         0  
 ffc                       1.6.0                    py27_2  
 fiat                      1.6.0                np19py27_1  
 fontconfig                2.11.1                        4  
 freetype                  2.5.2                         2  
 icu                       54.1                          0  
 instant                   1.6.0                    py27_2  
 libgfortran               1.0                           0  
 libpng                    1.6.17                        0  
 libxml2                   2.9.2                         0  
 llvm                      3.3                           0  
 mesa                      10.5.4                        0  
 mkl                       11.1                np19py27_p1  
 mkl-rt                    11.1                         p0  
 mkl-service               1.0.0                   py27_p2  
 mpi4py                    1.3.1                    py27_0  
 mpich2                    1.4.1p1                       0  
 nose                      1.3.7                    py27_0  
 numexpr                   2.4.4                np19py27_0  
 numpy                     1.9.3                    py27_0  
 openblas                  0.2.14                        3  
 openssl                   1.0.1k                        1  
 pcre                      8.31                          0  
 petsc                     3.5.2                    py27_2  
 petsc4py                  3.5.1                    py27_1  
 pip                       7.1.2                    py27_0  
 ply                       3.8                      py27_0  
 python                    2.7.10                        1  
 qt                        4.8.6                         3  
 readline                  6.2                           2  
 scikit-learn              0.16.1               np19py27_0  
 scipy                     0.16.0               np19py27_1  
 setuptools                18.3.2                   py27_0  
 six                       1.9.0                    py27_0  
 slepc                     3.5.4                    py27_1  
 sqlite                    3.8.4.1                       1  
 swig                      3.0.7                         0  
 sympy                     0.7.6.1                  py27_0  
 system                    5.8                           2  
 tk                        8.5.18                        0  
 ufl                       1.6.0                    py27_1  
 vtk                       6.3.0                    py27_0  
 wheel                     0.26.0                   py27_1  
 zlib                      1.2.8                         0  
 (fenics27) $
astrojuanlu commented 8 years ago

In that case, you have to downgrade VTK in the right environment and everything should woerk :) On Oct 9, 2015 12:31 PM, "e-aranda" notifications@github.com wrote:

Yes, you are right!

$ source activate fenics27 discarding /home/earanda/anaconda/bin from PATH prepending /home/earanda/anaconda/envs/fenics27/bin to PATH (fenics27)earanda@eranda-desktop:~$ conda list

packages in environment at /home/earanda/anaconda/envs/fenics27:

# boost 1.57.0 4 cmake 3.2.3 0 dolfin 1.6.0 py27_2 eigen3 3.2.1 1 fastcache 1.0.2 py27_0 fenics 1.6.0 0 ffc 1.6.0 py27_2 fiat 1.6.0 np19py27_1 fontconfig 2.11.1 4 freetype 2.5.2 2 icu 54.1 0 instant 1.6.0 py27_2 libgfortran 1.0 0 libpng 1.6.17 0 libxml2 2.9.2 0 llvm 3.3 0 mesa 10.5.4 0 mkl 11.1 np19py27_p1 mkl-rt 11.1 p0 mkl-service 1.0.0 py27_p2 mpi4py 1.3.1 py27_0 mpich2 1.4.1p1 0 nose 1.3.7 py27_0 numexpr 2.4.4 np19py27_0 numpy 1.9.3 py27_0 openblas 0.2.14 3 openssl 1.0.1k 1 pcre 8.31 0 petsc 3.5.2 py27_2 petsc4py 3.5.1 py27_1 pip 7.1.2 py27_0 ply 3.8 py27_0 python 2.7.10 1 qt 4.8.6 3 readline 6.2 2 scikit-learn 0.16.1 np19py27_0 scipy 0.16.0 np19py27_1 setuptools 18.3.2 py27_0 six 1.9.0 py27_0 slepc 3.5.4 py27_1 sqlite 3.8.4.1 1 swig 3.0.7 0 sympy 0.7.6.1 py27_0 system 5.8 2 tk 8.5.18 0 ufl 1.6.0 py27_1 vtk 6.3.0 py27_0 wheel 0.26.0 py27_1 zlib 1.2.8 0 (fenics27) $

— Reply to this email directly or view it on GitHub https://github.com/Juanlu001/fenics-recipes/issues/33#issuecomment-146829146 .

e-aranda commented 8 years ago

Yes!!!!

Thank you very much!!

astrojuanlu commented 8 years ago

Working on this, getting unrelated build errors now. Coraggio!