importing fenics fails because a shared libary is not made

[kociak]

Trying to import fenics generates the following traceback:

<ipython-input-4-743ea8bb985a> in <module>
----> 1 import fenics

/anaconda/envs/fenicsproject/lib/python3.7/site-packages/fenics/__init__.py in <module>
      5 """
      6 
----> 7 from dolfin import *

/anaconda/envs/fenicsproject/lib/python3.7/site-packages/dolfin/__init__.py in <module>
     32 
     33 # Import cpp modules
---> 34 from .cpp import __version__
     35 
     36 from .cpp.common import (Variable, has_debug, has_hdf5, has_scotch,

ImportError: dlopen(/anaconda/envs/fenicsproject/lib/python3.7/site-packages/dolfin/cpp.cpython-37m-darwin.so, 2): Library not loaded: @rpath/libdmumps-5.1.2.dylib
  Referenced from: /anaconda/envs/fenicsproject/lib/libpetsc.3.11.dylib
  Reason: image not found

Environment

``` appnope 0.1.0 py37_1000 conda-forge backcall 0.1.0 py_0 conda-forge blas 1.1 openblas conda-forge boost-cpp 1.70.0 hd59e818_0 conda-forge bzip2 1.0.6 h1de35cc_1002 conda-forge ca-certificates 2019.6.16 hecc5488_0 conda-forge certifi 2019.6.16 py37_0 conda-forge cmake 3.14.5 hdd2e4aa_0 conda-forge curl 7.64.1 h22ea746_0 conda-forge decorator 4.4.0 py_0 conda-forge eigen 3.3.7 h04f5b5a_1000 conda-forge expat 2.2.5 h6de7cb9_1003 conda-forge fastcache 1.1.0 py37h01d97ff_0 conda-forge fenics 2019.1.0 py37_3 conda-forge fenics-dijitso 2019.1.0 py_3 conda-forge fenics-dolfin 2019.1.0 py37hf5af79d_3 conda-forge fenics-ffc 2019.1.0 py_3 conda-forge fenics-fiat 2019.1.0 py_3 conda-forge fenics-libdolfin 2019.1.0 h733b22e_3 conda-forge fenics-ufl 2019.1.0 py_3 conda-forge gmp 6.1.2 h0a44026_1000 conda-forge gmpy2 2.1.0b1 py37h1744cca_0 conda-forge hdf5 1.10.4 mpi_mpich_h2f3dee2_1006 conda-forge hypre 2.15.1 he0087a8_1001 conda-forge icu 58.2 h0a44026_1000 conda-forge ipykernel 5.1.1 py37h24bf2e0_0 conda-forge ipython 7.6.1 py37h5ca1d4c_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jedi 0.14.0 py37_0 conda-forge jupyter_client 5.3.0 py_0 conda-forge jupyter_core 4.4.0 py_0 conda-forge krb5 1.16.3 hcfa6398_1001 conda-forge libblas 3.8.0 5_hd44dcd8_netlib conda-forge libcblas 3.8.0 5_hd44dcd8_netlib conda-forge libcurl 7.64.1 h16faf7d_0 conda-forge libcxx 8.0.0 4 conda-forge libcxxabi 8.0.0 4 conda-forge libedit 3.1.20170329 hcfe32e1_1001 conda-forge libffi 3.2.1 h6de7cb9_1006 conda-forge libgfortran 3.0.1 0 conda-forge libiconv 1.15 h01d97ff_1005 conda-forge liblapack 3.8.0 5_hd44dcd8_netlib conda-forge libsodium 1.0.17 h01d97ff_0 conda-forge libssh2 1.8.2 hcdc9a53_2 conda-forge libuv 1.30.1 h01d97ff_0 conda-forge metis 5.1.0 h0a44026_1003 conda-forge mpc 1.1.0 h3aece09_1006 conda-forge mpfr 4.0.2 h0a95893_0 conda-forge mpi 1.0 mpich conda-forge mpi4py 3.0.1 py37h77202c6_0 conda-forge mpich 3.2.1 ha90c164_1012 conda-forge mpmath 1.1.0 py_0 conda-forge mumps-mpi 5.1.2 blas_openblash9fe1a0a_1001 [blas_openblas] conda-forge ncurses 6.1 h0a44026_1002 conda-forge numpy 1.15.4 py37_blas_openblash4251c03_1000 [blas_openblas] conda-forge openblas 0.3.3 hdc02c5d_1001 conda-forge openssl 1.1.1b h01d97ff_2 conda-forge parmetis 4.0.3 hc4b10a8_1002 conda-forge parso 0.5.0 py_0 conda-forge petsc 3.11.1 hf985393_1 conda-forge petsc4py 3.11.0 py37hc745293_0 conda-forge pexpect 4.7.0 py37_0 conda-forge pickleshare 0.7.5 py37_1000 conda-forge pip 19.1.1 py37_0 conda-forge pkg-config 0.29.2 h112b980_1005 conda-forge pkgconfig 1.3.1 py37_1001 conda-forge prompt_toolkit 2.0.9 py_0 conda-forge ptscotch 6.0.6 ha54644a_1002 conda-forge ptyprocess 0.6.0 py_1001 conda-forge pybind11 2.2.4 py37h770b8ee_1001 conda-forge pygments 2.4.2 py_0 conda-forge python 3.7.3 h93065d6_1 conda-forge python-dateutil 2.8.0 py_0 conda-forge pyzmq 17.1.2 py37hae99301_0 conda-forge readline 8.0 hcfe32e1_0 conda-forge rhash 1.3.6 h1de35cc_1001 conda-forge scalapack 2.0.2 h2db4217_1005 conda-forge scotch 6.0.6 hde27766_1002 conda-forge setuptools 41.0.1 py37_0 conda-forge six 1.12.0 py37_1000 conda-forge slepc 3.11.1 h5bdb03d_0 conda-forge slepc4py 3.11.0 py37hc459697_0 conda-forge sqlite 3.28.0 hb7d70f7_1 conda-forge suitesparse 4.5.6 blas_openblash0bd06e0_1201 [blas_openblas] conda-forge sympy 1.4 py37_0 conda-forge tbb 2019.7 h770b8ee_0 conda-forge tk 8.6.9 h2573ce8_1002 conda-forge tornado 6.0.3 py37h01d97ff_0 conda-forge traitlets 4.3.2 py37_1000 conda-forge wcwidth 0.1.7 py_1 conda-forge wheel 0.33.4 py37_0 conda-forge xz 5.2.4 h1de35cc_1001 conda-forge zeromq 4.2.5 hfc679d8_4 conda-forge zlib 1.2.11 h1de35cc_1004 conda-forge (fenicsproject) MacBook-Pro-39:~ mathieukociak$ ```

running Mac OS X 10.14.3

Details about conda and system ( conda info ):

``` active environment : fenicsproject active env location : /anaconda/envs/fenicsproject shell level : 1 user config file : /Users/mathieukociak/.condarc populated config files : /Users/mathieukociak/.condarc conda version : 4.7.5 conda-build version : not installed python version : 3.6.7.final.0 virtual packages : base environment : /anaconda (writable) channel URLs : https://conda.anaconda.org/anaconda-fusion/osx-64 https://conda.anaconda.org/anaconda-fusion/noarch https://conda.anaconda.org/conda-forge/osx-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /anaconda/pkgs /Users/mathieukociak/.conda/pkgs envs directories : /anaconda/envs /Users/mathieukociak/.conda/envs platform : osx-64 user-agent : conda/4.7.5 requests/2.19.1 CPython/3.6.7 Darwin/18.2.0 OSX/10.14.3 UID:GID : 503:20 netrc file : None offline mode : False ```

[minrk]

Try upgrading fenics and petsc:

conda install fenics petsc

I think the latest builds should fix this

[minrk]

Verified fix:

conda create -yq -n fenics -c conda-forge
conda run -n fenics python -c 'import fenics'

(base) root@1eb172c57f5a:/# conda list -n fenics

``` # packages in environment at /opt/conda/envs/fenics: # # Name Version Build Channel _libgcc_mutex 0.1 main binutils_impl_linux-64 2.31.1 h6176602_1 binutils_linux-64 2.31.1 h6176602_8 boost-cpp 1.70.0 h8e57a91_2 conda-forge bzip2 1.0.8 h516909a_0 conda-forge ca-certificates 2019.6.16 hecc5488_0 conda-forge certifi 2019.6.16 py37_1 conda-forge cmake 3.15.1 hf94ab9c_0 conda-forge curl 7.65.3 hf8cf82a_0 conda-forge eigen 3.3.7 h6bb024c_1000 conda-forge expat 2.2.5 he1b5a44_1003 conda-forge fastcache 1.1.0 py37h516909a_0 conda-forge fenics 2019.1.0 py37_4 conda-forge fenics-dijitso 2019.1.0 py_4 conda-forge fenics-dolfin 2019.1.0 py37h2a49381_4 conda-forge fenics-ffc 2019.1.0 py_4 conda-forge fenics-fiat 2019.1.0 py_4 conda-forge fenics-libdolfin 2019.1.0 h9041177_4 conda-forge fenics-ufl 2019.1.0 py_4 conda-forge gcc_impl_linux-64 7.3.0 habb00fd_1 conda-forge gcc_linux-64 7.3.0 h553295d_8 conda-forge gmp 6.1.2 hf484d3e_1000 conda-forge gmpy2 2.1.0b1 py37h04dde30_0 conda-forge gxx_impl_linux-64 7.3.0 hdf63c60_1 conda-forge gxx_linux-64 7.3.0 h553295d_8 conda-forge hdf5 1.10.4 mpi_mpich_ha7d0aea_1006 conda-forge hypre 2.15.1 hc98498a_1001 conda-forge icu 64.2 he1b5a44_0 conda-forge krb5 1.16.3 h05b26f9_1001 conda-forge libblas 3.8.0 11_openblas conda-forge libcblas 3.8.0 11_openblas conda-forge libcurl 7.65.3 hda55be3_0 conda-forge libedit 3.1.20170329 hf8c457e_1001 conda-forge libffi 3.2.1 he1b5a44_1006 conda-forge libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_0 liblapack 3.8.0 11_openblas conda-forge libopenblas 0.3.6 h6e990d7_6 conda-forge libssh2 1.8.2 h22169c7_2 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0 libuv 1.30.1 h516909a_0 conda-forge metis 5.1.0 hf484d3e_1003 conda-forge mpc 1.1.0 hb20f59a_1006 conda-forge mpfr 4.0.2 ha14ba45_0 conda-forge mpi 1.0 mpich conda-forge mpi4py 3.0.1 py37hf046da1_0 conda-forge mpich 3.2.1 hc99cbb1_1013 conda-forge mpmath 1.1.0 py_0 conda-forge mumps-include 5.2.1 0 conda-forge mumps-mpi 5.2.1 h5bebb2f_0 conda-forge ncurses 6.1 hf484d3e_1002 conda-forge numpy 1.16.4 py37h95a1406_0 conda-forge openssl 1.1.1c h516909a_0 conda-forge parmetis 4.0.3 hb1a587f_1002 conda-forge petsc 3.11.3 h624fa55_0 conda-forge petsc4py 3.11.0 py37h906564f_0 conda-forge pip 19.2.1 py37_0 conda-forge pkg-config 0.29.2 h14c3975_1005 conda-forge pkgconfig 1.3.1 py37_1001 conda-forge ptscotch 6.0.6 h5a4526e_1002 conda-forge pybind11 2.2.4 py37hc9558a2_1001 conda-forge python 3.7.3 h33d41f4_1 conda-forge readline 8.0 hf8c457e_0 conda-forge rhash 1.3.6 h14c3975_1001 conda-forge scalapack 2.0.2 h2831592_1005 conda-forge scotch 6.0.6 h491eb26_1002 conda-forge setuptools 41.0.1 py37_0 conda-forge six 1.12.0 py37_1000 conda-forge slepc 3.11.2 h00d104f_0 conda-forge slepc4py 3.11.0 py37hce3d510_0 conda-forge sqlite 3.29.0 hcee41ef_0 conda-forge suitesparse 4.5.6 heab0a99_1202 conda-forge sympy 1.4 py37_0 conda-forge tbb 2019.7 hc9558a2_0 conda-forge tk 8.6.9 hed695b0_1002 conda-forge wheel 0.33.4 py37_0 conda-forge xz 5.2.4 h14c3975_1001 conda-forge zlib 1.2.11 h516909a_1005 conda-forge ```