conda-forge / fenics-feedstock

A conda-smithy repository for fenics.

About fenics-pkgs-feedstock

Feedstock license: BSD-3-Clause

Home: http://www.fenicsproject.org

Package license: LGPL-3.0-or-later

Summary: FEniCS is a collection of free software for automated, efficient solution of differential equations

Development: https://bitbucket.org/fenics-project/

Documentation: https://fenics.readthedocs.io/

FEniCS is a collection of free software for automated, efficient solution of differential equations (http://fenicsproject.org). It provides C++ and Python interfaces, and creates effecient solvers via expression of finite variational statements in a domain-specific language that are transformed and just-in-time compiled into efficient implementations.

Current build status

Azure

Variant Status linux_64_mpimpichnumpy1.22python3.10.____cpython linux_64_mpimpichnumpy1.22python3.9.____cpython linux_64_mpimpichnumpy1.23python3.11.____cpython linux_64_mpimpichnumpy1.26python3.12.____cpython linux_64_mpiopenmpinumpy1.22python3.10.____cpython linux_64_mpiopenmpinumpy1.22python3.9.____cpython linux_64_mpiopenmpinumpy1.23python3.11.____cpython linux_64_mpiopenmpinumpy1.26python3.12.____cpython linux_aarch64_mpimpichnumpy1.22python3.10.____cpython linux_aarch64_mpimpichnumpy1.22python3.9.____cpython linux_aarch64_mpimpichnumpy1.23python3.11.____cpython linux_aarch64_mpimpichnumpy1.26python3.12.____cpython linux_aarch64_mpiopenmpinumpy1.22python3.10.____cpython linux_aarch64_mpiopenmpinumpy1.22python3.9.____cpython linux_aarch64_mpiopenmpinumpy1.23python3.11.____cpython linux_aarch64_mpiopenmpinumpy1.26python3.12.____cpython linux_ppc64le_mpimpichnumpy1.22python3.10.____cpython linux_ppc64le_mpimpichnumpy1.22python3.9.____cpython linux_ppc64le_mpimpichnumpy1.23python3.11.____cpython linux_ppc64le_mpimpichnumpy1.26python3.12.____cpython linux_ppc64le_mpiopenmpinumpy1.22python3.10.____cpython linux_ppc64le_mpiopenmpinumpy1.22python3.9.____cpython linux_ppc64le_mpiopenmpinumpy1.23python3.11.____cpython linux_ppc64le_mpiopenmpinumpy1.26python3.12.____cpython osx_64_mpimpichnumpy1.22python3.10.____cpython osx_64_mpimpichnumpy1.22python3.9.____cpython osx_64_mpimpichnumpy1.23python3.11.____cpython osx_64_mpimpichnumpy1.26python3.12.____cpython osx_64_mpiopenmpinumpy1.22python3.10.____cpython osx_64_mpiopenmpinumpy1.22python3.9.____cpython osx_64_mpiopenmpinumpy1.23python3.11.____cpython osx_64_mpiopenmpinumpy1.26python3.12.____cpython osx_arm64_mpimpichnumpy1.22python3.10.____cpython osx_arm64_mpimpichnumpy1.22python3.9.____cpython osx_arm64_mpimpichnumpy1.23python3.11.____cpython osx_arm64_mpimpichnumpy1.26python3.12.____cpython osx_arm64_mpiopenmpinumpy1.22python3.10.____cpython osx_arm64_mpiopenmpinumpy1.22python3.9.____cpython osx_arm64_mpiopenmpinumpy1.23python3.11.____cpython osx_arm64_mpiopenmpinumpy1.26python3.12.____cpython

Current release info

Name	Downloads	Version	Platforms

Installing fenics-pkgs

Installing fenics-pkgs from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, fenics, fenics-dolfin, fenics-libdolfin can be installed with conda:

conda install fenics fenics-dolfin fenics-libdolfin

or with mamba:

mamba install fenics fenics-dolfin fenics-libdolfin

It is possible to list all of the versions of fenics available on your platform with conda:

conda search fenics --channel conda-forge

or with mamba:

mamba search fenics --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search fenics --channel conda-forge

# List packages depending on `fenics`:
mamba repoquery whoneeds fenics --channel conda-forge

# List dependencies of `fenics`:
mamba repoquery depends fenics --channel conda-forge

About conda-forge

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge anaconda.org channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating fenics-pkgs-feedstock

If you would like to improve the fenics-pkgs recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/fenics-pkgs-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

• If the version of a package is not being increased, please add or increase the build/number.
• If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

• @garth-wells
• @jan-janssen
• @johannesring
• @mikaem
• @minrk

fenics-feedstock's Issues

MUMPS seems to be super slow on Ubuntu 18

Not sure if this is the right place to ask. I modified the fenics hyperelastic demo to make it with 768k tets (80x80x20 intervals).

On Ubuntu 18, I use Anaconda3 fenics package with MUMPS. Per Newton step, it took about 10 min per Newton step (one direct solve) whether or not MPI is used (when using MPI I used -np 8, the machine is with 8 cores 16 threads).

On my macbook with Anaconda fenics (same version: 2018.1.0), one Newton step took a minute or so, though parallel didn't help much either.

Not sure what's causing the difference.

Thanks

Not compatible with latest `mshr` available on Conda.

Hi,

The latest version 2017.2.0 of FEniCS available is not compatible with the latest version 2017.1.0 of mshr. This breaks the FEniCS Julia bindings.

repackage using pybind11-2.3.0

There is a bug fix in pybind11 (see pybind/pybind11#1211) that allows fenics code to be used in a multi threaded python script. Without this fix there is a deadlock if fenics code is run outside of the main thread.

It would be nice to update to the latest version of pybind11 (2.3.0), where this issue is fixed. Currently 2.2.4 is installed.

FEniCS 2017.2.0 imcomptible with SymPy 1.2

Issue:
Hi,
Fenics-JIT compiler is not compatible with latest version of SymPy. Could you fix the dependancies tree ?

https://www.allanswered.com/post/qwqwo/#rrxrr

Best regards,

Environment (conda list):

packages in environment at /home/myname/.conda/envs/FEniCS:

blas 1.1 openblas conda-forge
boost 1.66.0 py27_1 conda-forge
boost-cpp 1.66.0 1 conda-forge
bzip2 1.0.6 1 conda-forge
ca-certificates 2018.4.16 0 conda-forge
certifi 2018.4.16 py27_0 conda-forge
cloog 0.18.0 0
cmake 3.11.4 0 conda-forge
curl 7.60.0 0 conda-forge
eigen 3.3.3 0 conda-forge
expat 2.2.5 0 conda-forge
fastcache 1.0.2 py27_0 conda-forge
fenics 2017.2.0 np113py27_3 conda-forge
gcc 4.8.5 7
gmp 6.1.2 0 conda-forge
gmpy2 2.0.8 py27_1 conda-forge
hdf5 1.10.1 2 conda-forge
hypre 2.11.2 1 conda-forge
icu 58.2 hfc679d8_0 conda-forge
isl 0.12.2 0
krb5 1.14.6 0 conda-forge
libgcc 5.2.0 0
libgcc-ng 7.2.0 hdf63c60_3 anaconda
libgfortran 3.0.0 1
libgfortran-ng 7.2.0 hdf63c60_3 anaconda
libopenblas 0.2.20 h9ac9557_7 anaconda
libssh2 1.8.0 2 conda-forge
libstdcxx-ng 7.2.0 hdf63c60_3 anaconda
libuv 1.20.3 0 conda-forge
metis 5.1.0 h470a237_3 conda-forge
mkl 2017.0.3 0
mpc 1.1.0 4 conda-forge
mpfr 3.1.5 0 conda-forge
mpi 1.0 mpich conda-forge
mpich 3.2.1 h26a2512_4 conda-forge
mpmath 1.0.0 py_0 conda-forge
mumps-mpi 5.0.2 blas_openblas_0 [blas_openblas] conda-forge
ncurses 5.9 10 conda-forge
numpy 1.13.3 py27_blas_openblas_201 [blas_openblas] conda-forge
numpy-base 1.14.3 py27h0ea5e3f_1 anaconda
openblas 0.2.20 8 conda-forge
openssl 1.0.2o 0 conda-forge
parmetis 4.0.3 hf0665dc_2 conda-forge
pcre 8.41 1 conda-forge
petsc 3.8.4 blas_openblas_0 [blas_openblas] conda-forge
petsc4py 3.8.1 py27_1 conda-forge
pip 9.0.3 py27_0 conda-forge
pkg-config 0.29.2 1 conda-forge
ply 3.11 py_1 conda-forge
ptscotch 6.0.4 3 conda-forge
python 2.7.15 0 conda-forge
readline 7.0 0 conda-forge
rhash 1.3.4 0 conda-forge
scalapack 2.0.2 h186ce0b_3 conda-forge
scotch 6.0.5 h9c0d707_1 conda-forge
setuptools 40.0.0 py27_0 conda-forge
six 1.11.0 py27_1 conda-forge
slepc 3.8.3 blas_openblas_0 [blas_openblas] conda-forge
slepc4py 3.8.0 py27_0 conda-forge
sqlite 3.20.1 2 conda-forge
subprocess32 3.2.7 py27_0
suitesparse 4.5.4 blas_openblas_201 [blas_openblas] conda-forge
swig 3.0.12 2 conda-forge
sympy 1.2 py27_0 conda-forge
tbb 2018_20171205 0 conda-forge
tk 8.6.7 0 conda-forge
wheel 0.31.1 py27_0 conda-forge
xz 5.2.3 0 conda-forge
zlib 1.2.11 0 conda-forge

$ conda list

Details about conda and system ( conda info ):

$ conda info

runtime dependencies

I doubt swig, cmake, gcc, eigen, pkg-config are runtime dependencies.
If boost is not linked it should be removed also.

FileNotFoundError: [Errno 2] No such file or directory: 'c++': 'c++' in miniconda3 image with user-agent Linux/4.15.0-50-generic

Issue:
Hi,
I know about the Docker image of fenics and have used it. But I need fenics now in combination with scipy in a newer version. So I thought of installing fenics in the miniconda3 image via this Dockerfile

FROM continuumio/miniconda3:4.6.14

RUN ["/bin/bash", "-c", "conda config --add channels conda-forge"]
RUN ["/bin/bash", "-c", "conda install numpy scipy matplotlib pandas scikit-learn"]
RUN ["/bin/bash", "-c", "conda install -v fenics fenics-dijitso fenics-dolfin fenics-ffc fenics-fiat fenics-libdolfin fenics-ufl"]
RUN ["/bin/bash", "-c", "mkdir /home/fenics"]
RUN ["/bin/bash", "-c", "mkdir /home/fenics/shared"]

WORKDIR /home/fenics/shared
ENTRYPOINT ["/bin/bash", "-c"]
CMD ["/bin/bash"]

On my local Windows 10 machine this works and my python code is exectued without errors. But when I build an image with this Dockerfile on our Linux server machine I get this error message:

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/opt/conda/lib/python3.7/multiprocessing/pool.py", line 121, in worker
    result = (True, func(*args, **kwds))
  File "/opt/conda/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
    return list(map(*args))
  File "adv_fit_direct_to_exp.py", line 118, in multip
    result_r = minimizer(error_func_r, bounds)
  File "/opt/conda/lib/python3.7/site-packages/scipy/optimize/_dual_annealing.py", line 631, in dual_annealing
    energy_state.reset(func_wrapper, rand_state, x0)
  File "/opt/conda/lib/python3.7/site-packages/scipy/optimize/_dual_annealing.py", line 174, in reset
    self.current_energy = func_wrapper.fun(self.current_location)
  File "/opt/conda/lib/python3.7/site-packages/scipy/optimize/_dual_annealing.py", line 374, in fun
    return self.func(x, *self.args)
  File "adv_fit_direct_to_exp.py", line 59, in func
    min_r=r[0], num_r=len(r)-1, num_t=len(t)
  File "/home/fenics/shared/biofilm-dye-diffusion/fenics_solver.py", line 53, in solve_pde
    V = FunctionSpace(mesh, 'P', 1)
  File "/opt/conda/lib/python3.7/site-packages/dolfin/function/functionspace.py", line 33, in __init__
    self._init_convenience(*args, **kwargs)
  File "/opt/conda/lib/python3.7/site-packages/dolfin/function/functionspace.py", line 100, in _init_convenience
    self._init_from_ufl(mesh, element, constrained_domain=constrained_domain)
  File "/opt/conda/lib/python3.7/site-packages/dolfin/function/functionspace.py", line 43, in _init_from_ufl
    mpi_comm=mesh.mpi_comm())
  File "/opt/conda/lib/python3.7/site-packages/dolfin/jit/jit.py", line 47, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/opt/conda/lib/python3.7/site-packages/dolfin/jit/jit.py", line 97, in ffc_jit
    return ffc.jit(ufl_form, parameters=p)
  File "/opt/conda/lib/python3.7/site-packages/ffc/jitcompiler.py", line 217, in jit
    module = jit_build(ufl_object, module_name, parameters)
  File "/opt/conda/lib/python3.7/site-packages/ffc/jitcompiler.py", line 133, in jit_build
    generate=jit_generate)
  File "/opt/conda/lib/python3.7/site-packages/dijitso/jit.py", line 178, in jit
    params)
  File "/opt/conda/lib/python3.7/site-packages/dijitso/build.py", line 153, in build_shared_library
    status, output = get_status_output(cmd)
  File "/opt/conda/lib/python3.7/site-packages/dijitso/system.py", line 41, in _get_status_output_subprocess
    stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
  File "/opt/conda/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/opt/conda/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'c++': 'c++'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "adv_fit_direct_to_exp.py", line 187, in <module>
    main()
  File "adv_fit_direct_to_exp.py", line 184, in main
    p.map(multip, l)
  File "/opt/conda/lib/python3.7/multiprocessing/pool.py", line 268, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/opt/conda/lib/python3.7/multiprocessing/pool.py", line 657, in get
    raise self._value
FileNotFoundError: [Errno 2] No such file or directory: 'c++': 'c++'

The only difference I found between the two images ist via the conda info. The
windows machine has

Linux/4.14.111-boot2docker

while the Linux server machine has

Linux/4.15.0-50-generic

in the user-agent output. See below for the full output. How can I fix this issue and is this really related to the different user-agents?


Environment (conda list):

Windows 10 machine

# packages in environment at /opt/conda:
#
# Name                    Version                   Build  Channel
asn1crypto                0.24.0                   py37_0
binutils_impl_linux-64    2.31.1               h6176602_1
binutils_linux-64         2.31.1               h6176602_7
boost-cpp                 1.70.0               ha2d47e9_0    conda-forge
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2019.3.9             hecc5488_0    conda-forge
certifi                   2019.3.9                 py37_0    conda-forge
cffi                      1.12.2           py37h2e261b9_1
chardet                   3.0.4                    py37_1
cmake                     3.14.5               hf94ab9c_0    conda-forge
conda                     4.6.14                   py37_0    conda-forge
cryptography              2.6.1            py37h1ba5d50_0
curl                      7.64.1               hf8cf82a_0    conda-forge
cycler                    0.10.0                     py_1    conda-forge
dbus                      1.13.2               h714fa37_1
eigen                     3.3.7             h6bb024c_1000    conda-forge
expat                     2.2.5             hf484d3e_1002    conda-forge
fastcache                 1.1.0            py37h516909a_0    conda-forge
fenics                    2019.1.0                 py37_2    conda-forge
fenics-dijitso            2019.1.0                   py_2    conda-forge
fenics-dolfin             2019.1.0         py37h80b64ce_2    conda-forge
fenics-ffc                2019.1.0                   py_2    conda-forge
fenics-fiat               2019.1.0                   py_2    conda-forge
fenics-libdolfin          2019.1.0             h9041177_2    conda-forge
fenics-ufl                2019.1.0                   py_2    conda-forge
fontconfig                2.13.1            he4413a7_1000    conda-forge
freetype                  2.10.0               he983fc9_0    conda-forge
gcc_impl_linux-64         7.3.0                habb00fd_1    conda-forge
gcc_linux-64              7.3.0                h553295d_7    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
glib                      2.56.2            had28632_1001    conda-forge
gmp                       6.1.2             hf484d3e_1000    conda-forge
gmpy2                     2.0.8           py37hb20f59a_1002    conda-forge
gst-plugins-base          1.14.0               hbbd80ab_1
gstreamer                 1.14.0               hb453b48_1
gxx_impl_linux-64         7.3.0                hdf63c60_1    conda-forge
gxx_linux-64              7.3.0                h553295d_7    conda-forge
hdf5                      1.10.4          mpi_mpich_ha7d0aea_1006    conda-forge
hypre                     2.15.1            hc98498a_1001    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
idna                      2.8                      py37_0
joblib                    0.13.2                     py_0    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
kiwisolver                1.1.0            py37hc9558a2_0    conda-forge
krb5                      1.16.3            h05b26f9_1001    conda-forge
libblas                   3.8.0                7_openblas    conda-forge
libcblas                  3.8.0                7_openblas    conda-forge
libcurl                   7.64.1               hda55be3_0    conda-forge
libedit                   3.1.20181209         hc058e9b_0
libffi                    3.2.1                hd88cf55_4
libgcc-ng                 8.2.0                hdf63c60_1
libgfortran-ng            7.3.0                hdf63c60_0
libiconv                  1.15              h516909a_1005    conda-forge
liblapack                 3.8.0                7_openblas    conda-forge
libpng                    1.6.37               hed695b0_0    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              8.2.0                hdf63c60_1
libuuid                   2.32.1            h14c3975_1000    conda-forge
libuv                     1.29.1               h516909a_0    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.9                h13577e0_0    conda-forge
matplotlib                3.1.0                    py37_1    conda-forge
matplotlib-base           3.1.0            py37hfd891ef_1    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_1010    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
mumps-include             5.1.2                      1007    conda-forge
mumps-mpi                 5.1.2             h5bebb2f_1007    conda-forge
ncurses                   6.1                  he6710b0_1
numpy                     1.15.4          py37h8b7e671_1002    conda-forge
openblas                  0.3.5             h9ac9557_1001    conda-forge
openssl                   1.1.1b               h14c3975_1    conda-forge
pandas                    0.24.2           py37hb3f55d8_0    conda-forge
parmetis                  4.0.3             hb1a587f_1002    conda-forge
pcre                      8.43                 he6710b0_0
petsc                     3.11.1               h624fa55_1    conda-forge
petsc4py                  3.11.0           py37h906564f_0    conda-forge
pip                       19.0.3                   py37_0
pkg-config                0.29.2            h14c3975_1005    conda-forge
pkgconfig                 1.3.1                 py37_1001    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptscotch                  6.0.6             h5a4526e_1002    conda-forge
pybind11                  2.2.4           py37hc9558a2_1001    conda-forge
pycosat                   0.6.3            py37h14c3975_0
pycparser                 2.19                     py37_0
pyopenssl                 19.0.0                   py37_0
pyparsing                 2.4.0                      py_0    conda-forge
pyqt                      5.6.0           py37h13b7fb3_1008    conda-forge
pysocks                   1.6.8                    py37_0
python                    3.7.3                h0371630_0
python-dateutil           2.8.0                      py_0    conda-forge
pytz                      2019.1                     py_0    conda-forge
qt                        5.6.3                h8bf5577_3
readline                  7.0                  h7b6447c_5
requests                  2.21.0                   py37_0
rhash                     1.3.6             h14c3975_1001    conda-forge
ruamel_yaml               0.15.46          py37h14c3975_0
scalapack                 2.0.2             h2831592_1005    conda-forge
scikit-learn              0.21.2           py37h627018c_0    conda-forge
scipy                     1.3.0            py37h921218d_0    conda-forge
scotch                    6.0.6             h491eb26_1002    conda-forge
setuptools                41.0.0                   py37_0
sip                       4.18.1          py37hf484d3e_1000    conda-forge
six                       1.12.0                   py37_0
slepc                     3.11.1               h00d104f_0    conda-forge
slepc4py                  3.11.0           py37hce3d510_0    conda-forge
sqlite                    3.27.2               h7b6447c_0
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
tornado                   6.0.2            py37h516909a_0    conda-forge
urllib3                   1.24.1                   py37_0
wheel                     0.33.1                   py37_0
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xz                        5.2.4                h14c3975_4
yaml                      0.1.7                had09818_2
zlib                      1.2.11               h7b6447c_3

Linux machine

# packages in environment at /opt/conda:
#
# Name                    Version                   Build  Channel
asn1crypto                0.24.0                   py37_0
binutils_impl_linux-64    2.31.1               h6176602_1
binutils_linux-64         2.31.1               h6176602_7
boost-cpp                 1.68.0            h11c811c_1000    conda-forge
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2019.3.9             hecc5488_0    conda-forge
certifi                   2019.3.9                 py37_0    conda-forge
cffi                      1.12.2           py37h2e261b9_1
chardet                   3.0.4                    py37_1
cmake                     3.14.5               hf94ab9c_0    conda-forge
conda                     4.6.14                   py37_0    conda-forge
cryptography              2.6.1            py37h1ba5d50_0
curl                      7.64.1               hf8cf82a_0    conda-forge
cycler                    0.10.0                     py_1    conda-forge
dbus                      1.13.2               h714fa37_1
eigen                     3.3.7             h6bb024c_1000    conda-forge
expat                     2.2.5             hf484d3e_1002    conda-forge
fastcache                 1.1.0            py37h516909a_0    conda-forge
fenics                    2019.1.0                 py37_1    conda-forge
fenics-dijitso            2019.1.0                   py_2    conda-forge
fenics-dolfin             2019.1.0         py37h1c4d066_1    conda-forge
fenics-ffc                2019.1.0                   py_2    conda-forge
fenics-fiat               2019.1.0                   py_2    conda-forge
fenics-libdolfin          2019.1.0             h370d018_1    conda-forge
fenics-ufl                2019.1.0                   py_2    conda-forge
fontconfig                2.13.1            he4413a7_1000    conda-forge
freetype                  2.10.0               he983fc9_0    conda-forge
gcc_impl_linux-64         7.3.0                habb00fd_1    conda-forge
gcc_linux-64              7.3.0                h553295d_7    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
glib                      2.56.2            had28632_1001    conda-forge
gmp                       6.1.2             hf484d3e_1000    conda-forge
gmpy2                     2.0.8           py37hb20f59a_1002    conda-forge
gst-plugins-base          1.14.0               hbbd80ab_1
gstreamer                 1.14.0               hb453b48_1
gxx_impl_linux-64         7.3.0                hdf63c60_1    conda-forge
gxx_linux-64              7.3.0                h553295d_7    conda-forge
hdf5                      1.10.4          mpi_mpich_ha7d0aea_1006    conda-forge
hypre                     2.15.1            hc98498a_1001    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
idna                      2.8                      py37_0
joblib                    0.13.2                     py_0    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
kiwisolver                1.1.0            py37hc9558a2_0    conda-forge
krb5                      1.16.3            h05b26f9_1001    conda-forge
libblas                   3.8.0                7_openblas    conda-forge
libcblas                  3.8.0                7_openblas    conda-forge
libcurl                   7.64.1               hda55be3_0    conda-forge
libedit                   3.1.20181209         hc058e9b_0
libffi                    3.2.1                hd88cf55_4
libgcc-ng                 8.2.0                hdf63c60_1
libgfortran-ng            7.3.0                hdf63c60_0
libiconv                  1.15              h516909a_1005    conda-forge
liblapack                 3.8.0                7_openblas    conda-forge
libpng                    1.6.37               hed695b0_0    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              8.2.0                hdf63c60_1
libuuid                   2.32.1            h14c3975_1000    conda-forge
libuv                     1.29.1               h516909a_0    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.9                h13577e0_0    conda-forge
matplotlib                3.1.0                    py37_1    conda-forge
matplotlib-base           3.1.0            py37hfd891ef_1    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_1010    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
mumps-include             5.1.2                      1007    conda-forge
mumps-mpi                 5.1.2             h5bebb2f_1007    conda-forge
ncurses                   6.1                  he6710b0_1
numpy                     1.15.4          py37h8b7e671_1002    conda-forge
openblas                  0.3.5             h9ac9557_1001    conda-forge
openssl                   1.1.1b               h14c3975_1    conda-forge
pandas                    0.24.2           py37hb3f55d8_0    conda-forge
parmetis                  4.0.3             hb1a587f_1002    conda-forge
pcre                      8.43                 he6710b0_0
petsc                     3.11.1               h624fa55_1    conda-forge
petsc4py                  3.11.0           py37h906564f_0    conda-forge
pip                       19.0.3                   py37_0
pkg-config                0.29.2            h14c3975_1005    conda-forge
pkgconfig                 1.3.1                 py37_1001    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptscotch                  6.0.6             h5a4526e_1002    conda-forge
pybind11                  2.2.4           py37hc9558a2_1001    conda-forge
pycosat                   0.6.3            py37h14c3975_0
pycparser                 2.19                     py37_0
pyopenssl                 19.0.0                   py37_0
pyparsing                 2.4.0                      py_0    conda-forge
pyqt                      5.6.0           py37h13b7fb3_1008    conda-forge
pysocks                   1.6.8                    py37_0
python                    3.7.3                h0371630_0
python-dateutil           2.8.0                      py_0    conda-forge
pytz                      2019.1                     py_0    conda-forge
qt                        5.6.3                h8bf5577_3
readline                  7.0                  h7b6447c_5
requests                  2.21.0                   py37_0
rhash                     1.3.6             h14c3975_1001    conda-forge
ruamel_yaml               0.15.46          py37h14c3975_0
scalapack                 2.0.2             h2831592_1005    conda-forge
scikit-learn              0.21.2           py37h627018c_0    conda-forge
scipy                     1.3.0            py37h921218d_0    conda-forge
scotch                    6.0.6             h491eb26_1002    conda-forge
setuptools                41.0.0                   py37_0
sip                       4.18.1          py37hf484d3e_1000    conda-forge
six                       1.12.0                   py37_0
slepc                     3.11.1               h00d104f_0    conda-forge
slepc4py                  3.11.0           py37hce3d510_0    conda-forge
sqlite                    3.27.2               h7b6447c_0
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
tornado                   6.0.2            py37h516909a_0    conda-forge
urllib3                   1.24.1                   py37_0
wheel                     0.33.1                   py37_0
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xz                        5.2.4                h14c3975_4
yaml                      0.1.7                had09818_2
zlib                      1.2.11               h7b6447c_3

Details about conda and system ( conda info ):

Windows 10 machine

     active environment : base
    active env location : /opt/conda
            shell level : 1
       user config file : /root/.condarc
 populated config files : /root/.condarc
          conda version : 4.6.14
    conda-build version : not installed
         python version : 3.7.3.final.0
       base environment : /opt/conda  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/conda/pkgs
                          /root/.conda/pkgs
       envs directories : /opt/conda/envs
                          /root/.conda/envs
               platform : linux-64
             user-agent : conda/4.6.14 requests/2.21.0 CPython/3.7.3 Linux/4.14.111-boot2docker debian/9 glibc/2.24
                UID:GID : 0:0
             netrc file : None
           offline mode : False

Linux machine

     active environment : base
    active env location : /opt/conda
            shell level : 1
       user config file : /root/.condarc
 populated config files : /root/.condarc
          conda version : 4.6.14
    conda-build version : not installed
         python version : 3.7.3.final.0
       base environment : /opt/conda  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/conda/pkgs
                          /root/.conda/pkgs
       envs directories : /opt/conda/envs
                          /root/.conda/envs
               platform : linux-64
             user-agent : conda/4.6.14 requests/2.21.0 CPython/3.7.3 Linux/4.15.0-50-generic debian/9 glibc/2.24
                UID:GID : 0:0
             netrc file : None
           offline mode : False

Problem with superlu_dist 6/7

• I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

I am having problems installing fenics from conda-forge. The problematic package is "superlu_dist", which recently had version 7 available on conda-forge. The error was the following:

ImportError: libsuperlu_dist.so.6: cannot open shared object file: No such file or directory

The solution to this problem was to pin the dependency of superlu_dist to <= 6.2.0, which was also done in this repo.

However, my CI tests today failed, again due to superlu_dist. Now, however, superlust_dist = 6.2.0 was installed, but the error is:

ImportError: libsuperlu_dist.so.7: cannot open shared object file: No such file or directory

when I try to import fenics. To me, it seems like using superlu_dist >= 7.0.0 would and should be possible.

As this occured during my CI build, you can check the logs here: https://github.com/sblauth/cashocs/runs/4247175888?check_suite_focus=true

Environment (conda list):

$ conda list

Details about conda and system ( conda info ):

$ conda info

build with PETSc

once PETSc is building, we should link dolfin with PETSc

conda-forge/staged-recipes#1488

Rebuild FEniCS against PETSc with MUMPS

Although PETSc is now built with MUMPS, running dolfin.list_linear_solver_methods() shows that MUMPS is not available:

>>> import dolfin
>>> dolfin.list_linear_solver_methods()
Solver method  |  Description                                               
----------------------------------------------------------------------------
bicgstab       |  Biconjugate gradient stabilized method                    
cg             |  Conjugate gradient method                                 
default        |  default linear solver                                     
gmres          |  Generalized minimal residual method                       
minres         |  Minimal residual method                                   
petsc          |  PETSc built in LU solver                                  
richardson     |  Richardson method                                         
tfqmr          |  Transpose-free quasi-minimal residual method              
umfpack        |  UMFPACK (Unsymmetric MultiFrontal sparse LU factorization)
>>> 

This is likely because the latest FEniCS package was built before the PETSc package was built with MUMPS. Looking at the build log for fenics shows that it was built with petsc 3.8.3-blas_openblas_0, while MUMPS support in petsc was first added in 3.8.3-blas_openblas_1. Rebuilding fenics should fix this issue.

FEniCS should depend on specific SWIG version

FEniCS should depend on a specific SWIG version or else it will lead to problems like this.

Fenics needs OpenBLAS and doesn't work with MKL

Somehow Fenics doesn't work with MKL and forces to use OpenBLAS.

See microsoft/qmt#132

Unable to install fenics with conda install - install process terminates with error

OS: Ubuntu 20.04 LTS on 64-bit machine

Issue: I try to install fenics / libdmumps / fenics related packages in a conda environment and it results in termination of the install process with errors

Environment (# packages in environment at /home/blueskies/miniconda3/envs/fenics: # conda --version conda 4.9.0 # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge ca-certificates 2020.6.20 hecda079_0 conda-forge certifi 2020.6.20 py38h924ce5b_2 conda-forge ld_impl_linux-64 2.35 h769bd43_9 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-ng 9.3.0 h5dbcf3e_17 conda-forge libgomp 9.3.0 h5dbcf3e_17 conda-forge libstdcxx-ng 9.3.0 h2ae2ef3_17 conda-forge ncurses 6.2 he1b5a44_2 conda-forge openssl 1.1.1h h516909a_0 conda-forge pip 20.2.4 py_0 conda-forge python 3.8.6 h852b56e_0_cpython conda-forge python_abi 3.8 1_cp38 conda-forge readline 8.0 he28a2e2_2 conda-forge setuptools 49.6.0 py38h924ce5b_2 conda-forge sqlite 3.33.0 h4cf870e_1 conda-forge tk 8.6.10 hed695b0_1 conda-forge wheel 0.35.1 pyh9f0ad1d_0 conda-forge xz 5.2.5 h516909a_1 conda-forge zlib 1.2.11 h516909a_1010 conda-forge ):

Details about code run to install different libraries conda install -c conda-forge fenics conda install -c conda-forge libdmumps conda install -c conda-forge fenics fenics-dijitso fenics-dolfin fenics-ffc fenics-fiat fenics-libdolfin fenics-ufl

and


system ( active environment : fenics
active env location : /home/blueskies/miniconda3/envs/fenics
shell level : 2
user config file : /home/blueskies/.condarc
populated config files : /home/blueskies/.condarc
conda version : 4.9.0
conda-build version : 3.20.4
python version : 3.8.6.final.0
virtual packages : __glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/blueskies/miniconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/blueskies/miniconda3/pkgs
/home/blueskies/.conda/pkgs
envs directories : /home/blueskies/miniconda3/envs
/home/blueskies/.conda/envs
platform : linux-64
user-agent : conda/4.9.0 requests/2.24.0 CPython/3.8.6 Linux/5.4.0-52-generic ubuntu/20.04.1 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False ):

Errors generated (fenics) blueskies@sz-HP15-Nb:~$ conda install fenics fenics-dijitso fenics-dolfin fenics-ffc fenics-fiat fenics-libdolfin fenics-ufl Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): failed

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
    return getattr(module, func_name)(args, parser)
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/cli/main_install.py", line 20, in execute
    install(args, parser, 'install')
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/cli/install.py", line 261, in install
    unlink_link_transaction = solver.solve_for_transaction(
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 114, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 157, in solve_for_diff
    final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 262, in solve_final_state
    ssc = self._collect_all_metadata(ssc)
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 425, in _collect_all_metadata
    index, r = self._prepare(prepared_specs)
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 1020, in _prepare
    reduced_index = get_reduced_index(self.prefix, self.channels,
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/index.py", line 276, in get_reduced_index
    new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 120, in query_all
    result = tuple(concat(executor.map(subdir_query, channel_urls)))
  File "/home/blueskies/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 611, in result_iterator
    yield fs.pop().result()
  File "/home/blueskies/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 432, in result
    return self.__get_result()
  File "/home/blueskies/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
    raise self._exception
  File "/home/blueskies/miniconda3/lib/python3.8/concurrent/futures/thread.py", line 57, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 112, in <lambda>
    subdir_query = lambda url: tuple(SubdirData(Channel(url), repodata_fn=repodata_fn).query(
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 125, in query
    self.load()
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 189, in load
    _internal_state = self._load()
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 251, in _load
    _internal_state = self._read_local_repdata(mod_etag_headers.get('_etag'),
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 326, in _read_local_repdata
    _internal_state = self._process_raw_repodata_str(raw_repodata_str)
  File "/home/blueskies/miniconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 364, in _process_raw_repodata_str
    json_obj = json.loads(raw_repodata_str or '{}')
  File "/home/blueskies/miniconda3/lib/python3.8/json/__init__.py", line 357, in loads
    return _default_decoder.decode(s)
  File "/home/blueskies/miniconda3/lib/python3.8/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/blueskies/miniconda3/lib/python3.8/json/decoder.py", line 353, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Invalid control character at: line 85395 column 54 (char 2467927)

$ /home/blueskies/miniconda3/bin/conda install fenics fenics-dijitso fenics-dolfin fenics-ffc fenics-fiat fenics-libdolfin fenics-ufl

environment variables:
CIO_TEST=
CONDA_DEFAULT_ENV=fenics
CONDA_EXE=/home/blueskies/miniconda3/bin/conda
CONDA_PREFIX=/home/blueskies/miniconda3/envs/fenics
CONDA_PREFIX_1=/home/blueskies/miniconda3
CONDA_PROMPT_MODIFIER=(fenics)
CONDA_PYTHON_EXE=/home/blueskies/miniconda3/bin/python
CONDA_ROOT=/home/blueskies/miniconda3
CONDA_SHLVL=2
CURL_CA_BUNDLE=
PATH=/home/blueskies/miniconda3/bin:/home/blueskies/miniconda3/envs/fenics/bi
n:/home/blueskies/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/u
sr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session1

 active environment : fenics
active env location : /home/blueskies/miniconda3/envs/fenics
        shell level : 2
   user config file : /home/blueskies/.condarc

populated config files : /home/blueskies/.condarc
conda version : 4.9.0
conda-build version : 3.20.4
python version : 3.8.6.final.0
virtual packages : __glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/blueskies/miniconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/blueskies/miniconda3/pkgs
/home/blueskies/.conda/pkgs
envs directories : /home/blueskies/miniconda3/envs
/home/blueskies/.conda/envs
platform : linux-64
user-agent : conda/4.9.0 requests/2.24.0 CPython/3.8.6 Linux/5.4.0-52-generic ubuntu/20.04.1 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?


hi, I did upgrade my anaconda and i encounter these errors, may i ask for help on solving these errors?

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
If your shell is Bash or a Bourne variant, enable conda for the current user with

$ echo ". C:\Users\Lenovo\Anaconda3/etc/profile.d/conda.sh" >> ~/.bashrc

or, for all users, enable conda with

$ sudo ln -s C:\Users\Lenovo\Anaconda3/etc/profile.d/conda.sh /etc/profile.d/conda.sh

The options above will permanently enable the 'conda' command, but they do NOT
put conda's base (root) environment on PATH. To do so, run

$ conda activate

in your terminal, or to put the base environment on PATH permanently, run

$ echo "conda activate" >> ~/.bashrc

Previous to conda 4.4, the recommended way to activate conda was to modify PATH in
your ~/.bashrc file. You should manually remove the line that looks like

export PATH="C:\Users\Lenovo\Anaconda3/bin:$PATH"

^^^ The above line should NO LONGER be in your ~/.bashrc file! ^^^

Fenics ImportError: No module named _common

Issue:

I am trying to install fenics into an existing conda environment. I can install fenics without problems, but when I try to import it from within the environment, I get an error message:

No module named _common.

My environment is cellmodeller:

$ conda info --envs
# conda environments:
#
base                  *  /Users/user/anaconda2
cellmodeller             /Users/user/anaconda2/envs/cellmodeller

I installed fenics using

conda install --name cellmodeller -c conda-forge fenics

which gave no errors.
However, when I try to import fenics from within my cellmodeller environment, I get the following error message:

./anaconda2/envs/cellmodeller/bin/python2.7 -c 'from fenics import *'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/user/anaconda2/envs/cellmodeller/lib/python2.7/site-packages/fenics/__init__.py", line 7, in <module>
    from dolfin import *
  File "/Users/user/anaconda2/envs/cellmodeller/lib/python2.7/site-packages/dolfin/__init__.py", line 17, in <module>
    from . import cpp
  File "/Users/user/anaconda2/envs/cellmodeller/lib/python2.7/site-packages/dolfin/cpp/__init__.py", line 43, in <module>
    exec("from . import %s" % module_name)
  File "<string>", line 1, in <module>
  File "/Users/user/anaconda2/envs/cellmodeller/lib/python2.7/site-packages/dolfin/cpp/common.py", line 21, in <module>
    _common = swig_import_helper()
  File "/Users/user/anaconda2/envs/cellmodeller/lib/python2.7/site-packages/dolfin/cpp/common.py", line 20, in swig_import_helper
    return importlib.import_module('_common')
  File "/Users/user/anaconda2/envs/cellmodeller/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
ImportError: No module named _common

Does anyone have any ideas? I've seen similar errors listed before here and here. In the latter case, it was suggested that reverting boost version would solve the problem. I tried this using

conda install --name cellmodeller -c conda-forge boost=1.61

which ran successfully, but I still get a similar error when trying to import fenics as above.
Can anyone help?

Environment (conda list):

$ conda list

packages in environment at /Users/user/anaconda2:
_ipyw_jlab_nb_ext_conf    0.1.0            py27h172cb35_0  
alabaster                 0.7.10           py27h9dd7d6e_0  
anaconda                  custom           py27h2cfa9e9_0    anaconda
anaconda-client           1.6.5            py27hc13fba8_0  
anaconda-navigator        1.6.9            py27h103b016_0  
anaconda-project          0.8.0            py27h9e3d455_0  
appnope                   0.1.0            py27hb466136_0  
appscript                 1.0.1            py27h451298e_1  
asn1crypto                0.22.0           py27h61af4a7_1  
astroid                   1.5.3            py27h96f3fd4_0  
astropy                   2.0.2            py27h87cc2bd_4  
babel                     2.5.0            py27h7311c9e_0  
backports                 1.0              py27hb4f9756_1  
backports.functools_lru_cache 1.4              py27h2aca819_1  
backports.shutil_get_terminal_size 1.0.0            py27hc9115de_2  
backports_abc             0.5              py27h6972548_0  
beautifulsoup4            4.6.0            py27h9416283_1  
bitarray                  0.8.1            py27hd5bfd95_0  
bkcharts                  0.2              py27haafc882_0  
blas                      1.1                    openblas    conda-forge
blaze                     0.11.3           py27hb49378a_0  
bleach                    2.0.0            py27ha7d1710_0  
bokeh                     0.12.10          py27hf91827b_0  
boost                     1.66.0                   py27_1    conda-forge
boost-cpp                 1.66.0                        1    conda-forge
boto                      2.48.0           py27hacdd0fd_1  
bottleneck                1.2.1            py27h71f98a3_0  
bzip2                     1.0.6                h92991f9_1  
ca-certificates           2018.10.15           ha4d7672_0    conda-forge
cdecimal                  2.3              py27hf5d9fd9_1  
certifi                   2018.10.15            py27_1000    conda-forge
cffi                      1.10.0           py27haac214c_1  
chardet                   3.0.4            py27h2842e91_1  
click                     6.7              py27h2b86a94_0  
cloudpickle               0.4.0            py27h665dddb_0  
clyent                    1.2.2            py27hc0ae608_0  
cmake                     3.9.4                h30c3106_0  
colorama                  0.3.9            py27hbbe92b6_0  
conda                     4.4.7                    py27_0    anaconda
conda-build               3.0.27           py27h7659b69_0  
conda-env                 2.6.0                h36134e3_0    anaconda
conda-verify              2.0.0            py27hbebe81d_0  
configparser              3.5.0            py27hc7edf1b_0  
contextlib2               0.5.5            py27h9cb85f4_0  
cryptography              2.0.3            py27hab69567_1  
curl                      7.55.1               h7601780_3  
cycler                    0.10.0           py27hfc73c78_0  
cython                    0.26.1           py27h6a053f9_0  
cytoolz                   0.8.2            py27ha56cda1_0  
dask                      0.15.3           py27h8a1b457_0  
dask-core                 0.15.3           py27h6a32bf4_0  
datashape                 0.5.4            py27hd6a1745_0  
dbus                      1.10.22              h50d9ad6_0  
decorator                 4.1.2            py27h9f877ea_0  
distributed               1.19.1           py27h67dd2ec_0  
docutils                  0.14             py27h0befae3_0  
eigen                     3.3.5                h2d50403_1    conda-forge
entrypoints               0.2.3            py27hd680fb1_2  
enum34                    1.1.6            py27hf475452_1  
et_xmlfile                1.0.1            py27hc42f929_0  
expat                     2.2.4                h8f26bf8_1  
fastcache                 1.0.2            py27hc4635c7_0  
fenics                    2017.2.0            np113py27_3    conda-forge
filelock                  2.0.12           py27h72fe922_0  
flask                     0.12.2           py27h3ac5568_0  
flask-cors                3.0.3            py27h13db576_0  
freetype                  2.8                  h143eb01_0  
funcsigs                  1.0.2            py27hb9f6266_0  
functools32               3.2.3.2          py27h8ceab06_1  
futures                   3.1.1            py27hb02a37a_0  
get_terminal_size         1.0.0                h7520d66_0  
gettext                   0.19.8.1             hb0f4f8b_2  
gevent                    1.2.2            py27hc02608c_0  
glib                      2.53.6               ha08cb78_1  
glob2                     0.5              py27h2f8fe13_0  
gmp                       6.1.2                h4a9834d_0  
gmpy2                     2.0.8            py27h7e2fca4_1  
greenlet                  0.4.12           py27h081ed54_0  
grin                      1.2.1            py27hc43e5f3_1  
h5py                      2.7.0            py27h217cc45_1  
hdf5                      1.10.1               h6090a45_0  
heapdict                  1.0.0            py27hb5e74ad_0  
html5lib                  0.999999999      py27hec7e2bc_0  
hypre                     2.11.2                        1    conda-forge
icu                       58.2                 hea21ae5_0  
idna                      2.6              py27hedea723_1  
imageio                   2.2.0            py27h37746d9_0  
imagesize                 0.7.1            py27h4f7bcc8_0  
intel-openmp              2018.0.0             h68bdfb3_7  
ipaddress                 1.0.18           py27h5b9a5b9_0  
ipykernel                 4.6.1            py27h1e70a78_0  
ipython                   5.4.1            py27h2b3d779_1  
ipython_genutils          0.2.0            py27h8b9a179_0  
ipywidgets                7.0.0            py27h3e52029_0  
isort                     4.2.15           py27h5bf637f_0  
itsdangerous              0.24             py27h3948ded_1  
jbig                      2.1                  h4d881f8_0  
jdcal                     1.3              py27hfeaf94f_0  
jedi                      0.10.2           py27hbb5dc62_0  
jinja2                    2.9.6            py27h92590e2_1  
jpeg                      9b                   haccd157_1  
jsonschema                2.6.0            py27hd9b497e_0  
jupyter                   1.0.0            py27hec63c99_0  
jupyter_client            5.1.0            py27hfaf569a_0  
jupyter_console           5.2.0            py27h9702a86_1  
jupyter_core              4.3.0            py27hd5161ba_0  
jupyterlab                0.27.0           py27h25d4955_2  
jupyterlab_launcher       0.4.0            py27he518b91_0  
lazy-object-proxy         1.3.1            py27h712ce3f_0  
libcxx                    4.0.1                h579ed51_0  
libcxxabi                 4.0.1                hebd6815_0  
libedit                   3.1                  hb4e282d_0  
libffi                    3.2.1                hd939716_3  
libgfortran               3.0.1                h93005f0_2  
libiconv                  1.15                 h99df5da_5  
libpng                    1.6.32               hce72d48_2  
libsodium                 1.0.13               hba5e272_2  
libssh2                   1.8.0                h1218725_2  
libtiff                   4.0.8                h8cd0352_9  
libuv                     1.23.2               h470a237_0    conda-forge
libxml2                   2.9.4                hbd0960b_5  
libxslt                   1.1.29               h95a2935_5  
llvmlite                  0.20.0                   py27_0  
locket                    0.2.0            py27ha10513d_1  
lxml                      4.1.0            py27hcb5f3a6_0  
lzo                       2.10                 hb6b8854_1  
markupsafe                1.0              py27hd3c86fa_1  
matplotlib                2.1.0            py27h3078195_0  
mccabe                    0.6.1            py27h1f69e8d_0  
metis                     5.1.0                h470a237_3    conda-forge
mistune                   0.7.4            py27h1658d75_0  
mkl                       2018.0.0             h5ef208c_6  
mkl-service               1.1.2            py27hcba3029_4  
mpc                       1.0.3                hc455b36_4  
mpfr                      3.1.5                h7fa3772_1  
mpi                       1.0                       mpich    conda-forge
mpich                     3.2.1                h26a2512_5    conda-forge
mpmath                    0.19             py27h09cdc99_2  
msgpack-python            0.4.8            py27h635ded4_0  
multipledispatch          0.4.9            py27h10993aa_0  
mumps-mpi                 5.0.2           blas_openblas_0  [blas_openblas]  conda-forge
navigator-updater         0.1.0            py27ha63e0b4_0  
nbconvert                 5.3.1            py27h6455e4c_0  
nbformat                  4.4.0            py27hddc86d0_0  
ncurses                   6.0                  ha932d30_1  
networkx                  2.0              py27h2503496_0  
nltk                      3.2.4            py27h1626047_0  
nose                      1.3.7            py27h2ee3cb8_2  
notebook                  5.0.0            py27h5f5981d_2  
numba                     0.35.0              np113py27_6  
numexpr                   2.6.2            py27h99e4b4f_1  
numpy                     1.13.3          py27_blas_openblas_201  [blas_openblas]  conda-forge
numpydoc                  0.7.0            py27h022f19e_0  
odo                       0.5.1            py27h992a9f7_0  
olefile                   0.44             py27h73ba740_0  
openblas                  0.2.20                        8    conda-forge
openpyxl                  2.4.8            py27h70e7ed9_1  
openssl                   1.0.2p               h470a237_1    conda-forge
packaging                 16.8             py27h24b219a_0  
pandas                    0.20.3           py27h2a3d8ca_2  
pandoc                    1.19.2.1             ha5e8f32_1  
pandocfilters             1.4.2            py27hed78c4e_1  
parmetis                  4.0.3                hf73f2d4_2    conda-forge
partd                     0.3.8            py27h7560dbf_0  
path.py                   10.3.1           py27h5e25276_0  
pathlib2                  2.3.0            py27he09da1e_0  
patsy                     0.4.1            py27h40ed276_0  
pcre                      8.41                 h29eefc5_0  
pep8                      1.7.0            py27hff3397c_0  
petsc                     3.8.4           blas_openblas_0  [blas_openblas]  conda-forge
petsc4py                  3.8.1                    py27_1    conda-forge
pexpect                   4.2.1            py27hc4e4961_0  
pickleshare               0.7.4            py27h37e3d41_0  
pillow                    4.2.1            py27h2cf1d5f_0  
pip                       9.0.1            py27h61def0c_3  
pkg-config                0.29.2               hf837533_3    conda-forge
pkginfo                   1.4.1            py27ha9221e7_0  
ply                       3.10             py27h6279b8a_0  
prompt_toolkit            1.0.15           py27h4a7b9c2_0  
psutil                    5.4.0            py27h7076ac6_0  
ptscotch                  6.0.4                         2    conda-forge
ptyprocess                0.5.2            py27h70f6364_0  
py                        1.4.34           py27h917aa57_1  
pyaudio                   0.2.7            py27h3777516_1  
pycodestyle               2.3.1            py27h5b634e0_0  
pycosat                   0.6.3            py27h6c51c7e_0    anaconda
pycparser                 2.18             py27h0d28d88_1  
pycrypto                  2.6.1            py27h4efa152_1  
pycurl                    7.43.0           py27h398a7fe_3  
pyflakes                  1.6.0            py27h4446e76_0  
pygments                  2.2.0            py27h1a556bb_0  
pylint                    1.7.4            py27hc678664_0  
pyodbc                    4.0.17           py27hc9de18c_0  
pyopenssl                 17.2.0           py27h732fe57_0  
pyparsing                 2.2.0            py27h5bb6aaf_0  
pyqt                      5.6.0            py27hf21fe59_6  
pysocks                   1.6.7            py27h1cff6a6_1  
pytables                  3.4.2            py27ha4551b8_2  
pytest                    3.2.1            py27h173df03_1  
python                    2.7.14              he768d2d_19  
python-dateutil           2.6.1            py27hd56c96b_1  
python.app                2                py27h84f57d0_6  
pytz                      2017.2           py27hb891d23_1  
pywavelets                0.5.2            py27hd99e88a_0  
pyyaml                    3.12             py27ha7932d0_1  
pyzmq                     16.0.2           py27he61c07e_2  
qt                        5.6.2               h9975529_14  
qtawesome                 0.4.4            py27hdeb2f59_0  
qtconsole                 4.3.1            py27hdc90b4f_0  
qtpy                      1.3.1            py27h39159f8_0  
readline                  7.0                  h81b24a6_3  
requests                  2.18.4           py27h9b2b37c_1  
rhash                     1.3.6                h470a237_1    conda-forge
rope                      0.10.5           py27he855d02_0  
ruamel_yaml               0.11.14          py27h31666c4_2  
scalapack                 2.0.2                h186ce0b_3    conda-forge
scandir                   1.6              py27h97aa1ee_0  
scikit-image              0.13.0           py27h03e84e1_1  
scikit-learn              0.19.1           py27h9788993_0  
scipy                     0.19.1           py27hf01dd8f_3  
seaborn                   0.8.0            py27h92884e4_0  
setuptools                36.5.0           py27h2a45cec_0  
simplegeneric             0.8.1            py27h6db5e31_0  
singledispatch            3.4.0.3          py27he22c18d_0  
sip                       4.18.1           py27h6300f65_2  
six                       1.11.0           py27h7252ba3_1  
slepc                     3.8.3           blas_openblas_0  [blas_openblas]  conda-forge
slepc4py                  3.8.0                    py27_0    conda-forge
snowballstemmer           1.2.1            py27h68ac032_0  
sortedcollections         0.5.3            py27h8094be4_0  
sortedcontainers          1.5.7            py27h322dbbf_0  
sphinx                    1.6.3            py27h11269f0_0  
sphinxcontrib             1.0              py27hd2ed746_1  
sphinxcontrib-websupport  1.0.1            py27h857890b_1  
spyder                    3.2.4            py27h93d9c3e_0  
sqlalchemy                1.1.13           py27hcbc9ed3_0  
sqlite                    3.20.1               h900c3b0_1  
ssl_match_hostname        3.5.0.1          py27h8780752_2  
statsmodels               0.8.0            py27h6d68dbf_0  
subprocess32              3.2.7            py27h24b2887_0  
suitesparse               4.5.4           blas_openblas_201  [blas_openblas]  conda-forge
swig                      3.0.12               hfc679d8_3    conda-forge
sympy                     1.1.1            py27hce55102_0  
tbb                       2019.1               h2d50403_0    conda-forge
tblib                     1.3.2            py27ha684fc4_0  
terminado                 0.6              py27he40bf16_0  
testpath                  0.3.1            py27h72d81a5_0  
tk                        8.6.7                hcdce994_1  
toolz                     0.8.2            py27h27228c4_0  
tornado                   4.5.2            py27h29aec9e_0  
traitlets                 4.3.2            py27hcf08151_0  
typing                    3.6.2            py27h646fea0_0  
unicodecsv                0.14.1           py27h170f95c_0  
unixodbc                  2.3.4                h4cb4dde_1  
urllib3                   1.22             py27hc3787e9_0  
vtk                       6.3.0                    py27_1    anaconda
wcwidth                   0.1.7            py27h817c265_0  
webencodings              0.5.1            py27h19a9f58_1  
werkzeug                  0.12.2           py27hcac71f8_0  
wheel                     0.29.0           py27h84bd1c0_1  
widgetsnbextension        3.0.2            py27h56f70de_1  
wrapt                     1.10.11          py27hd341262_0  
xlrd                      1.1.0            py27hbd41ed1_1  
xlsxwriter                1.0.2            py27h7f1064a_0  
xlwings                   0.11.4           py27h4d78f01_0  
xlwt                      1.2.0            py27hbeec4ae_0  
xz                        5.2.3                ha24016e_1  
yaml                      0.1.7                hff548bb_1  
zeromq                    4.2.2                h131e0f7_1  
zict                      0.1.3            py27h5fff8b1_0  
zlib                      1.2.11               h60db283_1  
zoo-wsmithpro:~ user$ 

Details about conda and system ( conda info ):

$ conda info
     active environment : None
       user config file : /Users/user/.condarc
 populated config files : /Users/user/.condarc
          conda version : 4.4.7
    conda-build version : 3.0.27
         python version : 2.7.14.final.0
       base environment : /Users/user/anaconda2  (writable)
           channel URLs : https://repo.continuum.io/pkgs/main/osx-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/osx-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/osx-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/osx-64
                          https://repo.continuum.io/pkgs/pro/noarch
          package cache : /Users/user/anaconda2/pkgs
                          /Users/user/.conda/pkgs
       envs directories : /Users/user/anaconda2/envs
                          /Users/user/.conda/envs
               platform : osx-64
             user-agent : conda/4.4.7 requests/2.18.4 CPython/2.7.14 Darwin/17.7.0 OSX/10.13.6
                UID:GID : 503:20
             netrc file : None
           offline mode : False

Error installing FEniCS on OS X

I had FEniCS installed on OS X El Capitan and it was working perfectly through Anaconda (Spyder), but it stopped working today, and when I tried to re-install FEniCS, i got the following error:

sophias-MacBook-Air:~ sophiaw$ conda install fenics
Traceback (most recent call last):
  File "/Users/sophiaw/anaconda/bin/conda", line 6, in <module>
    sys.exit(conda.cli.main())
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 94, in main
    imported = importlib.import_module(module)
  File "/Users/sophiaw/anaconda/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/cli/main_list.py", line 18, in <module>
    from ..egg_info import get_egg_info
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/egg_info.py", line 15, in <module>
    from .misc import rel_path
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/misc.py", line 18, in <module>
    from .instructions import RM_FETCHED, FETCH, RM_EXTRACTED, EXTRACT, UNLINK, LINK, SYMLINK_CONDA
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/instructions.py", line 7, in <module>
    from .fetch import fetch_pkg
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/fetch.py", line 13, in <module>
    import requests
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/__init__.py", line 60, in <module>
    from .packages.urllib3.exceptions import DependencyWarning
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/packages/__init__.py", line 29, in <module>
    import urllib3
ImportError: No module named urllib3
Using Anaconda API: https://api.anaconda.org
Fetching package metadata ...An unexpected error has occurred, please consider sending the
following traceback to the conda GitHub issue tracker at:

    https://github.com/conda/conda/issues

Include the output of the command 'conda info' in your report.


Traceback (most recent call last):
  File "/Users/sophiaw/anaconda/bin/conda", line 6, in <module>
    sys.exit(conda.cli.main())
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 120, in main
    exit_code = args_func(args, p)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 130, in args_func
    exit_code = args.func(args, p)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/cli/main_install.py", line 78, in execute
    install(args, parser, 'install')
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/cli/install.py", line 231, in install
    index = common.get_index_trap(**index_args)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/cli/common.py", line 627, in get_index_trap
    return get_index(*args, **kwargs)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/api.py", line 25, in get_index
    index = fetch_index(channel_urls, use_cache=use_cache, unknown=unknown)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/fetch.py", line 295, in fetch_index
    repodatas = [(u, f.result()) for u, f in zip(urls, futures)]
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/concurrent/futures/_base.py", line 405, in result
    return self.__get_result()
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/concurrent/futures/thread.py", line 55, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/fetch.py", line 68, in func
    res = f(*args, **kwargs)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/fetch.py", line 112, in fetch_repodata
    resp = session.get(url + filename, headers=headers, proxies=session.proxies)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/sessions.py", line 501, in get
    return self.request('GET', url, **kwargs)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/sessions.py", line 488, in request
    resp = self.send(prep, **send_kwargs)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/sessions.py", line 609, in send
    r = adapter.send(request, **kwargs)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/adapters.py", line 423, in send
    timeout=timeout
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/packages/urllib3/connectionpool.py", line 594, in urlopen
    chunked=chunked)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/packages/urllib3/connectionpool.py", line 350, in _make_request
    self._validate_conn(conn)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/packages/urllib3/connectionpool.py", line 835, in _validate_conn
    conn.connect()
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/packages/urllib3/connection.py", line 323, in connect
    ssl_context=context)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/packages/urllib3/util/ssl_.py", line 308, in ssl_wrap_socket
    context.load_verify_locations(ca_certs, ca_cert_dir)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/packages/urllib3/contrib/pyopenssl.py", line 392, in load_verify_locations
    self._ctx.load_verify_locations(cafile, capath)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/OpenSSL/SSL.py", line 525, in load_verify_locations
    _raise_current_error()
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/OpenSSL/_util.py", line 48, in exception_from_error_queue
    raise exception_type(errors)
OpenSSL.SSL.Error: [('system library', 'fopen', 'No such file or directory'), ('BIO routines', 'BIO_new_file', 'no such file'), ('x509 certificate routines', 'X509_load_cert_crl_file', 'system lib')]
sophias-MacBook-Air:~ sophiaw$ 

and here is the conda info:

sophias-MacBook-Air:~ sophiaw$ conda info
Traceback (most recent call last):
  File "/Users/sophiaw/anaconda/bin/conda", line 6, in <module>
    sys.exit(conda.cli.main())
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 94, in main
    imported = importlib.import_module(module)
  File "/Users/sophiaw/anaconda/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/cli/main_list.py", line 18, in <module>
    from ..egg_info import get_egg_info
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/egg_info.py", line 15, in <module>
    from .misc import rel_path
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/misc.py", line 18, in <module>
    from .instructions import RM_FETCHED, FETCH, RM_EXTRACTED, EXTRACT, UNLINK, LINK, SYMLINK_CONDA
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/instructions.py", line 7, in <module>
    from .fetch import fetch_pkg
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/conda/fetch.py", line 13, in <module>
    import requests
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/__init__.py", line 60, in <module>
    from .packages.urllib3.exceptions import DependencyWarning
  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/requests/packages/__init__.py", line 29, in <module>
    import urllib3
ImportError: No module named urllib3
Current conda install:

             platform : osx-64
        conda version : 4.1.12
    conda-env version : 2.6.0
  conda-build version : 2.0.2
       python version : 2.7.13.final.0
     requests version : 2.12.4
     root environment : /Users/sophiaw/anaconda  (writable)
  default environment : /Users/sophiaw/anaconda
     envs directories : /Users/sophiaw/anaconda/envs
        package cache : /Users/sophiaw/anaconda/pkgs
         channel URLs : https://conda.anaconda.org/conda-forge/osx-64/
                        https://conda.anaconda.org/conda-forge/noarch/
                        https://conda.anaconda.org/anaconda-fusion/osx-64/
                        https://conda.anaconda.org/anaconda-fusion/noarch/
                        https://repo.continuum.io/pkgs/free/osx-64/
                        https://repo.continuum.io/pkgs/free/noarch/
                        https://repo.continuum.io/pkgs/pro/osx-64/
                        https://repo.continuum.io/pkgs/pro/noarch/
          config file : /Users/sophiaw/.condarc
         offline mode : False
    is foreign system : False

anyway to fix this?

thank you,

Conda fenics with Gcc and python 2

Issue:

Downloading and Extracting Packages
sympy-1.4 | 9.9 MB | ################################################################################################################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: | ERROR conda.core.link:_execute_post_link_actions(658): An error occurred while installing package 'defaults::gcc-4.8.5-7'.
LinkError: post-link script failed for package defaults::gcc-4.8.5-7
running your command again with -v will provide additional information
location of failed script: /opt/anaconda2/envs/fenicsproject/bin/.gcc-post-link.sh
==> script messages <==

Attempting to roll back.

failed
ERROR conda.core.link:_execute(568): An error occurred while installing package 'defaults::gcc-4.8.5-7'.
LinkError: post-link script failed for package defaults::gcc-4.8.5-7
running your command again with -v will provide additional information
location of failed script: /opt/anaconda2/envs/fenicsproject/bin/.gcc-post-link.sh
==> script messages <==

Attempting to roll back.

Rolling back transaction: done

CondaMultiError: LinkError: post-link script failed for package defaults::gcc-4.8.5-7
running your command again with -v will provide additional information
location of failed script: /opt/anaconda2/envs/fenicsproject/bin/.gcc-post-link.sh
==> script messages <==

Environment (conda list):

WARNING: The conda.compat module is deprecated and will be removed in a future release.
# packages in environment at /opt/anaconda2:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py27_0  
alabaster                 0.7.12                   py27_0  
anaconda                  2019.03                  py27_0  
anaconda-client           1.7.2                    py27_0  
anaconda-navigator        1.9.7                    py27_0  
anaconda-project          0.8.2                    py27_0  
asn1crypto                0.24.0                   py27_0  
astroid                   1.6.5                    py27_0  
astropy                   2.0.9            py27hdd07704_0  
atomicwrites              1.3.0                    py27_1  
attrs                     19.1.0                   py27_1  
babel                     2.6.0                    py27_0  
backports                 1.0                      py27_1  
backports.functools_lru_cache 1.5                      py27_1  
backports.os              0.1.1                    py27_0  
backports.shutil_get_terminal_size 1.0.0                    py27_2  
backports_abc             0.5              py27h7b3c97b_0  
beautifulsoup4            4.7.1                    py27_1  
bitarray                  0.8.3            py27h14c3975_0  
bkcharts                  0.2              py27h241ae91_0  
blas                      1.0                         mkl  
bleach                    3.1.0                    py27_0  
blosc                     1.15.0               hd408876_0  
bokeh                     1.0.4                    py27_0  
boto                      2.49.0                   py27_0  
bottleneck                1.2.1            py27h035aef0_1  
bzip2                     1.0.6                h14c3975_5  
ca-certificates           2019.1.23                     0  
cairo                     1.14.12              h8948797_3  
cdecimal                  2.3              py27h14c3975_3  
certifi                   2019.3.9                 py27_0  
cffi                      1.12.2           py27h2e261b9_1  
chardet                   3.0.4                    py27_1  
click                     7.0                      py27_0  
cloudpickle               0.8.0                    py27_0  
clyent                    1.2.2                    py27_1  
colorama                  0.4.1                    py27_0  
conda                     4.6.11                   py27_0  
conda-build               3.17.8                   py27_0  
conda-env                 2.6.0                         1  
conda-verify              3.1.1                    py27_0  
configparser              3.7.3                    py27_1  
contextlib2               0.5.5            py27hbf4c468_0  
cryptography              2.6.1            py27h1ba5d50_0  
curl                      7.64.0               hbc83047_2  
cycler                    0.10.0           py27hc7354d3_0  
cython                    0.29.6           py27he6710b0_0  
cytoolz                   0.9.0.1          py27h14c3975_1  
dask                      1.1.4                    py27_1  
dask-core                 1.1.4                    py27_1  
dbus                      1.13.6               h746ee38_0  
decorator                 4.4.0                    py27_1  
defusedxml                0.5.0                    py27_1  
distributed               1.26.0                   py27_1  
docutils                  0.14             py27hae222c1_0  
entrypoints               0.3                      py27_0  
enum34                    1.1.6                    py27_1  
et_xmlfile                1.0.1            py27h75840f5_0  
expat                     2.2.6                he6710b0_0  
fastcache                 1.0.2            py27h14c3975_2  
filelock                  3.0.10                   py27_0  
flask                     1.0.2                    py27_1  
fontconfig                2.13.0               h9420a91_0  
freetype                  2.9.1                h8a8886c_1  
fribidi                   1.0.5                h7b6447c_0  
funcsigs                  1.0.2            py27h83f16ab_0  
functools32               3.2.3.2                  py27_1  
future                    0.17.1                   py27_0  
futures                   3.2.0                    py27_0  
get_terminal_size         1.0.0                haa9412d_0  
gevent                    1.4.0            py27h7b6447c_0  
glib                      2.56.2               hd408876_0  
glob2                     0.6                      py27_1  
gmp                       6.1.2                h6c8ec71_1  
gmpy2                     2.0.8            py27h10f8cd9_2  
graphite2                 1.3.13               h23475e2_0  
greenlet                  0.4.15           py27h7b6447c_0  
grin                      1.2.1                    py27_4  
gst-plugins-base          1.14.0               hbbd80ab_1  
gstreamer                 1.14.0               hb453b48_1  
h5py                      2.9.0            py27h7918eee_0  
harfbuzz                  1.8.8                hffaf4a1_0  
hdf5                      1.10.4               hb1b8bf9_0  
heapdict                  1.0.0                    py27_2  
html5lib                  1.0.1                    py27_0  
icu                       58.2                 h9c2bf20_1  
idna                      2.8                      py27_0  
imageio                   2.5.0                    py27_0  
imagesize                 1.1.0                    py27_0  
importlib_metadata        0.8                      py27_0  
intel-openmp              2019.3                      199  
ipaddress                 1.0.22                   py27_0  
ipykernel                 4.10.0                   py27_0  
ipython                   5.8.0                    py27_0  
ipython_genutils          0.2.0            py27h89fb69b_0  
ipywidgets                7.4.2                    py27_0  
isort                     4.3.16                   py27_0  
itsdangerous              1.1.0                    py27_0  
jbig                      2.1                  hdba287a_0  
jdcal                     1.4                      py27_0  
jedi                      0.13.3                   py27_0  
jinja2                    2.10                     py27_0  
jpeg                      9b                   h024ee3a_2  
jsonschema                3.0.1                    py27_0  
jupyter                   1.0.0                    py27_7  
jupyter_client            5.2.4                    py27_0  
jupyter_console           5.2.0                    py27_1  
jupyter_core              4.4.0                    py27_0  
jupyterlab                0.33.11                  py27_0  
jupyterlab_launcher       0.11.2           py27h28b3542_0  
kiwisolver                1.0.1            py27hf484d3e_0  
krb5                      1.16.1               h173b8e3_7  
lazy-object-proxy         1.3.1            py27h14c3975_2  
libarchive                3.3.3                h5d8350f_5  
libcurl                   7.64.0               h20c2e04_2  
libedit                   3.1.20181209         hc058e9b_0  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 8.2.0                hdf63c60_1  
libgfortran-ng            7.3.0                hdf63c60_0  
liblief                   0.9.0                h7725739_2  
libpng                    1.6.36               hbc83047_0  
libsodium                 1.0.16               h1bed415_0  
libssh2                   1.8.0                h1ba5d50_4  
libstdcxx-ng              8.2.0                hdf63c60_1  
libtiff                   4.0.10               h2733197_2  
libtool                   2.4.6                h7b6447c_5  
libuuid                   1.0.3                h1bed415_2  
libxcb                    1.13                 h1bed415_1  
libxml2                   2.9.9                he19cac6_0  
libxslt                   1.1.33               h7d1a2b0_0  
linecache2                1.0.0                    py27_0  
llvmlite                  0.28.0           py27hd408876_0  
locket                    0.2.0            py27h73929a2_1  
lxml                      4.3.2            py27hefd8a0e_0  
lz4-c                     1.8.1.2              h14c3975_0  
lzo                       2.10                 h49e0be7_2  
markupsafe                1.1.1            py27h7b6447c_0  
matplotlib                2.2.3            py27hb69df0a_0  
mccabe                    0.6.1                    py27_1  
mistune                   0.8.4            py27h7b6447c_0  
mkl                       2019.3                      199  
mkl-service               1.1.2            py27he904b0f_5  
mkl_fft                   1.0.10           py27ha843d7b_0  
mkl_random                1.0.2            py27hd81dba3_0  
more-itertools            5.0.0                    py27_0  
mpc                       1.1.0                h10f8cd9_1  
mpfr                      4.0.1                hdf1c602_3  
mpmath                    1.1.0                    py27_0  
msgpack-python            0.6.1            py27hfd86e86_1  
multipledispatch          0.6.0                    py27_0  
navigator-updater         0.2.1                    py27_0  
nbconvert                 5.4.1                    py27_3  
nbformat                  4.4.0            py27hed7f2b2_0  
ncurses                   6.1                  he6710b0_1  
networkx                  2.2                      py27_1  
nltk                      3.4                      py27_1  
nose                      1.3.7                    py27_2  
notebook                  5.7.8                    py27_0  
numba                     0.43.1           py27h962f231_0  
numexpr                   2.6.9            py27h9e4a6bb_0  
numpy                     1.16.2           py27h7e9f1db_0  
numpy-base                1.16.2           py27hde5b4d6_0  
numpydoc                  0.8.0                    py27_0  
olefile                   0.46                     py27_0  
openpyxl                  2.6.1                    py27_1  
openssl                   1.1.1b               h7b6447c_1  
packaging                 19.0                     py27_0  
pandas                    0.24.2           py27he6710b0_0  
pandoc                    2.2.3.2                       0  
pandocfilters             1.4.2                    py27_1  
pango                     1.42.4               h049681c_0  
parso                     0.3.4                    py27_0  
partd                     0.3.10                   py27_1  
patchelf                  0.9                  he6710b0_3  
path.py                   11.5.0                   py27_0  
pathlib2                  2.3.3                    py27_0  
patsy                     0.5.1                    py27_0  
pcre                      8.43                 he6710b0_0  
pep8                      1.7.1                    py27_0  
pexpect                   4.6.0                    py27_0  
pickleshare               0.7.5                    py27_0  
pillow                    5.4.1            py27h34e0f95_0  
pip                       19.0.3                   py27_0  
pixman                    0.38.0               h7b6447c_0  
pkginfo                   1.5.0.1                  py27_0  
pluggy                    0.9.0                    py27_0  
ply                       3.11                     py27_0  
prometheus_client         0.6.0                    py27_0  
prompt_toolkit            1.0.15           py27h1b593e1_0  
psutil                    5.6.1            py27h7b6447c_0  
ptyprocess                0.6.0                    py27_0  
py                        1.8.0                    py27_0  
py-lief                   0.9.0            py27h7725739_2  
pycairo                   1.18.0           py27h2a1e443_0  
pycodestyle               2.5.0                    py27_0  
pycosat                   0.6.3            py27h14c3975_0  
pycparser                 2.19                     py27_0  
pycrypto                  2.6.1            py27h14c3975_9  
pycurl                    7.43.0.2         py27h1ba5d50_0  
pyflakes                  2.1.1                    py27_0  
pygments                  2.3.1                    py27_0  
pylint                    1.9.2                    py27_0  
pyodbc                    4.0.26           py27he6710b0_0  
pyopenssl                 19.0.0                   py27_0  
pyparsing                 2.3.1                    py27_0  
pyqt                      5.9.2            py27h05f1152_2  
pyrsistent                0.14.11          py27h7b6447c_0  
pysocks                   1.6.8                    py27_0  
pytables                  3.5.1            py27h71ec239_0  
pytest                    4.3.1                    py27_0  
python                    2.7.16               h9bab390_0  
python-dateutil           2.8.0                    py27_0  
python-libarchive-c       2.8                      py27_6  
pytz                      2018.9                   py27_0  
pywavelets                1.0.2            py27hdd07704_0  
pyyaml                    5.1              py27h7b6447c_0  
pyzmq                     18.0.0           py27he6710b0_0  
qt                        5.9.7                h5867ecd_1  
qtawesome                 0.5.7                    py27_1  
qtconsole                 4.4.3                    py27_0  
qtpy                      1.7.0                    py27_1  
readline                  7.0                  h7b6447c_5  
requests                  2.21.0                   py27_0  
rope                      0.12.0                   py27_0  
ruamel_yaml               0.15.46          py27h14c3975_0  
scandir                   1.10.0           py27h7b6447c_0  
scikit-image              0.14.2           py27he6710b0_0  
scikit-learn              0.20.3           py27hd81dba3_0  
scipy                     1.2.1            py27h7c811a0_0  
seaborn                   0.9.0                    py27_0  
send2trash                1.5.0                    py27_0  
setuptools                40.8.0                   py27_0  
simplegeneric             0.8.1                    py27_2  
singledispatch            3.4.0.3          py27h9bcb476_0  
sip                       4.19.8           py27hf484d3e_0  
six                       1.12.0                   py27_0  
snappy                    1.1.7                hbae5bb6_3  
snowballstemmer           1.2.1            py27h44e2768_0  
sortedcollections         1.1.2                    py27_0  
sortedcontainers          2.1.0                    py27_0  
soupsieve                 1.8                      py27_0  
sphinx                    1.8.5                    py27_0  
sphinxcontrib             1.0                      py27_1  
sphinxcontrib-websupport  1.1.0                    py27_1  
spyder                    3.3.3                    py27_0  
spyder-kernels            0.4.2                    py27_0  
sqlalchemy                1.3.1            py27h7b6447c_0  
sqlite                    3.27.2               h7b6447c_0  
ssl_match_hostname        3.7.0.1                  py27_0  
statsmodels               0.9.0            py27h035aef0_0  
subprocess32              3.5.3            py27h7b6447c_0  
sympy                     1.3                      py27_0  
tblib                     1.3.2            py27h51fe5ba_0  
terminado                 0.8.1                    py27_1  
testpath                  0.4.2                    py27_0  
tk                        8.6.8                hbc83047_0  
toolz                     0.9.0                    py27_0  
tornado                   5.1.1            py27h7b6447c_0  
tqdm                      4.31.1                   py27_1  
traceback2                1.4.0                    py27_0  
traitlets                 4.3.2            py27hd6ce930_0  
typing                    3.6.6                    py27_0  
unicodecsv                0.14.1           py27h5062da9_0  
unittest2                 1.1.0                    py27_0  
unixodbc                  2.3.7                h14c3975_0  
urllib3                   1.24.1                   py27_0  
wcwidth                   0.1.7            py27h9e3e1ab_0  
webencodings              0.5.1                    py27_1  
werkzeug                  0.14.1                   py27_0  
wheel                     0.33.1                   py27_0  
widgetsnbextension        3.4.2                    py27_0  
wrapt                     1.11.1           py27h7b6447c_0  
wurlitzer                 1.0.2                    py27_0  
xlrd                      1.2.0                    py27_0  
xlsxwriter                1.1.5                    py27_0  
xlwt                      1.3.0            py27h3d85d97_0  
xz                        5.2.4                h14c3975_4  
yaml                      0.1.7                had09818_2  
zeromq                    4.3.1                he6710b0_3  
zict                      0.1.4                    py27_0  
zipp                      0.3.3                    py27_1  
zlib                      1.2.11               h7b6447c_3  
zstd                      1.3.7                h0b5b093_0 

Details about conda and system ( conda info ):

     active environment : None
       user config file : /Users/weizhang/software/ubuntu/.condarc
 populated config files : 
          conda version : 4.6.11
    conda-build version : 3.17.8
         python version : 2.7.16.final.0
       base environment : /opt/anaconda2  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/anaconda2/pkgs
                          /Users/weizhang/software/ubuntu/.conda/pkgs
       envs directories : /opt/anaconda2/envs
                          /Users/weizhang/software/ubuntu/.conda/envs
               platform : linux-64
             user-agent : conda/4.6.11 requests/2.21.0 CPython/2.7.16 Linux/4.9.125-linuxkit ubuntu/18.04 glibc/2.27
                UID:GID : 0:0
             netrc file : None
           offline mode : False

Add dev version

Would be helpful to have a dev version, since this package makes it easier to install on cloud services, which in turn will drive work on the dev version to enhance support for browser based visualisation.

enable MPI

now that we've got a feedstock, we should enable building with MPI

Installing mpi4py breaks JIT.

After installing Anaconda 4.3.1 and fenics from conda-forge, everything seems to work very well. The JIT works and the tests I have pass fine. However, I have received user requests for mpi4py with the install. After mpi4py is installed, JIT fails with the following error:

`"PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"

I have attached the complete compile log. I have redone the build without mpich on the system without any change to the result. Any advice on how to proceed would be most welcome.

compile.log.txt

`

RuntimeWarning: mpi4py.MPI.Prequest size changed

• I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

When running the python version of the Poisson demo, I see a lot of warnings like this:

  if MPI.size(mpi_comm) == 1:
/home/johannr/miniconda3/envs/fenics-test2/lib/python3.9/site-packages/dolfin/jit/jit.py:46: RuntimeWarning: mpi4py.MPI.Prequest size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject

Environment (conda list):

$ conda list
# packages in environment at /home/johannr/miniconda3/envs/fenics-test2:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
binutils_linux-64         2.36                 hf3e587d_1    conda-forge
boost-cpp                 1.74.0               h312852a_4    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.2               h7f98852_0    conda-forge
ca-certificates           2021.5.30            ha878542_0    conda-forge
certifi                   2021.5.30        py39hf3d152e_0    conda-forge
cmake                     3.21.2               h8897547_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
dbus                      1.13.6               h48d8840_2    conda-forge
eigen                     3.3.9                h4bd325d_1    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
fenics                    2019.1.0        py39hf3d152e_21    conda-forge
fenics-dijitso            2019.1.0        py39hf3d152e_21    conda-forge
fenics-dolfin             2019.1.0        py39hc6fefde_21    conda-forge
fenics-ffc                2019.1.0        py39hf3d152e_21    conda-forge
fenics-fiat               2019.1.0        py39hf3d152e_21    conda-forge
fenics-libdolfin          2019.1.0            h5ba192a_21    conda-forge
fenics-ufl                2019.1.0        py39hf3d152e_21    conda-forge
fontconfig                2.13.1            hba837de_1005    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
gcc_impl_linux-64         9.4.0                h03d3576_8    conda-forge
gcc_linux-64              9.4.0                h391b98a_1    conda-forge
gettext                   0.19.8.1          h73d1719_1006    conda-forge
glib                      2.68.4               h9c3ff4c_1    conda-forge
glib-tools                2.68.4               h9c3ff4c_1    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmpy2                     2.1.0b5          py39h78fa15d_0    conda-forge
gst-plugins-base          1.18.5               hf529b03_0    conda-forge
gstreamer                 1.18.5               h76c114f_0    conda-forge
gxx_impl_linux-64         9.4.0                h03d3576_8    conda-forge
gxx_linux-64              9.4.0                h0316aca_1    conda-forge
hdf5                      1.10.6          mpi_mpich_h996c276_1014    conda-forge
hypre                     2.18.2               hc98498a_1    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_14    conda-forge
kiwisolver                1.3.2            py39h1a9c180_0    conda-forge
krb5                      1.19.2               hcc1bbae_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      2.2.1                h9c3ff4c_0    conda-forge
libblas                   3.9.0           11_linux64_openblas    conda-forge
libcblas                  3.9.0           11_linux64_openblas    conda-forge
libclang                  11.1.0          default_ha53f305_1    conda-forge
libcurl                   7.79.0               h2574ce0_0    conda-forge
libdeflate                1.7                  h7f98852_5    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               hcdb4288_3    conda-forge
libffi                    3.4.2                h9c3ff4c_1    conda-forge
libgcc-devel_linux-64     9.4.0                hd854feb_8    conda-forge
libgcc-ng                 11.2.0               h1d223b6_8    conda-forge
libgfortran-ng            11.2.0               h69a702a_8    conda-forge
libgfortran5              11.2.0               h5c6108e_8    conda-forge
libglib                   2.68.4               h174f98d_1    conda-forge
libgomp                   11.2.0               h1d223b6_8    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           11_linux64_openblas    conda-forge
libllvm11                 11.1.0               hf817b99_2    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.17          pthreads_h8fe5266_1    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     13.3                 hd57d9b9_0    conda-forge
libsanitizer              9.4.0                h79bfe98_8    conda-forge
libssh2                   1.10.0               ha56f1ee_0    conda-forge
libstdcxx-devel_linux-64  9.4.0                hd854feb_8    conda-forge
libstdcxx-ng              11.2.0               he4da1e4_8    conda-forge
libtiff                   4.3.0                hf544144_1    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libuv                     1.42.0               h7f98852_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.2.1                h7f98852_0    conda-forge
libxcb                    1.13              h7f98852_1003    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
matplotlib                3.4.3            py39hf3d152e_0    conda-forge
matplotlib-base           3.4.3            py39h2fa2bec_0    conda-forge
metis                     5.1.0             h58526e2_1006    conda-forge
mpc                       1.2.1                h9f54685_0    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
mpi                       1.0                       mpich    conda-forge
mpi4py                    3.1.1            py39h6438238_0    conda-forge
mpich                     3.4.2              h846660c_100    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
mumps-include             5.2.1               ha770c72_10    conda-forge
mumps-mpi                 5.2.1               hd6b9cac_10    conda-forge
mysql-common              8.0.25               ha770c72_2    conda-forge
mysql-libs                8.0.25               hfa10184_2    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
nspr                      4.30                 h9c3ff4c_0    conda-forge
nss                       3.69                 hb5efdd6_0    conda-forge
numpy                     1.21.2           py39hdbf815f_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1l               h7f98852_0    conda-forge
parmetis                  4.0.3             h2a9763c_1005    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
petsc                     3.14.5               h60475ce_0    conda-forge
petsc4py                  3.14.1           py39h16c3f58_1    conda-forge
pillow                    8.3.2            py39ha612740_0    conda-forge
pip                       21.2.4             pyhd8ed1ab_0    conda-forge
pkg-config                0.29.2            h36c2ea0_1008    conda-forge
pkgconfig                 1.5.5            py39hf3d152e_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptscotch                  6.0.9                h253636d_1    conda-forge
pybind11                  2.6.2            py39h1a9c180_0    conda-forge
pybind11-global           2.6.2            py39h1a9c180_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyqt                      5.12.3           py39hf3d152e_7    conda-forge
pyqt-impl                 5.12.3           py39h0fcd23e_7    conda-forge
pyqt5-sip                 4.19.18          py39he80948d_7    conda-forge
pyqtchart                 5.12             py39h0fcd23e_7    conda-forge
pyqtwebengine             5.12.1           py39h0fcd23e_7    conda-forge
python                    3.9.7           hb7a2778_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
qt                        5.12.9               hda022c4_4    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
rhash                     1.4.1                h7f98852_0    conda-forge
scalapack                 2.0.2             hf659fdc_1009    conda-forge
scotch                    6.0.9                h3858553_1    conda-forge
setuptools                58.0.4           py39hf3d152e_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
slepc                     3.14.2               h44d3fa2_0    conda-forge
slepc4py                  3.14.0           py39h1e75aa9_1    conda-forge
sqlite                    3.36.0               h9cd32fc_1    conda-forge
suitesparse               5.6.0                h717dc36_0    conda-forge
superlu                   5.2.2                h16cfea0_0    conda-forge
superlu_dist              6.2.0                h25dcc4a_4    conda-forge
sympy                     1.8              py39hf3d152e_0    conda-forge
sysroot_linux-64          2.12                he073ed8_14    conda-forge
tbb                       2020.2               h4bd325d_4    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
tornado                   6.1              py39h3811e60_1    conda-forge
tzdata                    2021a                he74cb21_1    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge

Details about conda and system ( conda info ):

$ conda info

     active environment : fenics-test2
    active env location : /home/johannr/miniconda3/envs/fenics-test2
            shell level : 1
       user config file : /home/johannr/.condarc
 populated config files : /home/johannr/.condarc
          conda version : 4.10.0
    conda-build version : not installed
         python version : 3.9.1.final.0
       virtual packages : __linux=5.11.0=0
                          __glibc=2.33=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/johannr/miniconda3  (writable)
      conda av data dir : /home/johannr/miniconda3/etc/conda
  conda av metadata url : https://repo.anaconda.com/pkgs/main
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/johannr/miniconda3/pkgs
                          /home/johannr/.conda/pkgs
       envs directories : /home/johannr/miniconda3/envs
                          /home/johannr/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.0 requests/2.25.1 CPython/3.9.1 Linux/5.11.0-25-generic ubuntu/21.04 glibc/2.33
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

LD_LIBRARY_PATH not set correctly on environments

Issue:

When installing the fenics meta-package into a separate environment, the library paths are not set correctly: Installing fenics using conda create -n fenicsproject -c conda-forge fenics creates the following $CONDA_DIR/envs/fenicsproject/share/dolfin/dolfin.conf:

# Helper file for setting non-default DOLFIN environment variables

# Common Unix variables
export LD_LIBRARY_PATH=/opt/miniconda/envs/fenicsproject//opt/miniconda/envs/fenicsproject/lib:$LD_LIBRARY_PATH
export PATH=/opt/miniconda/envs/fenicsproject/bin:$PATH
export PKG_CONFIG_PATH=/opt/miniconda/envs/fenicsproject//opt/miniconda/envs/fenicsproject/lib/pkgconfig:$PKG_CONFIG_PATH
export MANPATH=/opt/miniconda/envs/fenicsproject/share/man:$MANPATH

# Special Mac variables
export DYLD_FRAMEWORK_PATH=/opt/local/Library/Frameworks:$DYLD_FRAMEWORK_PATH

(Note the double env prefix on the LD_LIBARY_PATH and PKG_CONFIG_PATH.)

With this dolfin.conf, typing

from dolfin import *
Expression("1",degree=0)

results in the error

dijitso failed to load existing file:
        /opt/miniconda/envs/fenicsproject/.cache/dijitso/lib/libdijitso-dolfin_expression_67128269551ba784c4d7d69f5f3ba722.so
error is:
        libmpicxx.so.12: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/opt/miniconda/envs/fenicsproject/lib/python3.7/site-packages/dolfin/jit/jit.py", line 168, in compile_class
    submodule = dijitso.extract_factory_function(module, "create_" + module_name)()
  File "/opt/miniconda/envs/fenicsproject/lib/python3.7/site-packages/dijitso/jit.py", line 47, in extract_factory_function
    function = getattr(lib, name)
AttributeError: 'NoneType' object has no attribute 'create_dolfin_expression_67128269551ba784c4d7d69f5f3ba722'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/miniconda/envs/fenicsproject/lib/python3.7/site-packages/dolfin/function/expression.py", line 400, in __init__
    self._cpp_object = jit.compile_expression(cpp_code, params)
  File "/opt/miniconda/envs/fenicsproject/lib/python3.7/site-packages/dolfin/function/jit.py", line 158, in compile_expression
    expression = compile_class(cpp_data, mpi_comm=mpi_comm)
  File "/opt/miniconda/envs/fenicsproject/lib/python3.7/site-packages/dolfin/jit/jit.py", line 170, in compile_class
    raise RuntimeError("Unable to compile C++ code with dijitso")
RuntimeError: Unable to compile C++ code with dijitso

Removing the double prefix fixes the problem.

link hdf5

fenics should link hdf5, but it should be a parallel build and conda-forge only has a serial hdf5 package.

cf conda-forge/hdf5-feedstock#51

ImportError: No module named _common

I tried to install fenics into conda env

name: fenics
channels:
  - conda-forge
dependencies:
  - python=2.7
  - anaconda==4.2
  - fenics=2016.1.0

and hit following import problem:

(fenics) desktop-rskolasinski:~> ipython
Python 2.7.12 | packaged by conda-forge | (default, Sep  8 2016, 14:22:31) 
Type "copyright", "credits" or "license" for more information.

IPython 5.1.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: import fenics
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-1ecb0c01ef73> in <module>()
----> 1 import fenics

/home/rskolasinski/miniconda3/envs/fenics/lib/python2.7/site-packages/fenics/__init__.py in <module>()
      5 """
      6 
----> 7 from dolfin import *

/home/rskolasinski/miniconda3/envs/fenics/lib/python2.7/site-packages/dolfin/__init__.pyc in <module>()
     15 
     16 # Import names from the compiled cpp modules
---> 17 from . import cpp
     18 from dolfin.cpp import *
     19 from dolfin.cpp import __version__, __swigversion__, __pythonversion__

/home/rskolasinski/miniconda3/envs/fenics/lib/python2.7/site-packages/dolfin/cpp/__init__.py in <module>()
     41 
     42     # Import the module
---> 43     exec("from . import %s" % module_name)
     44     module = globals()[module_name]
     45 

<string> in <module>()

/home/rskolasinski/miniconda3/envs/fenics/lib/python2.7/site-packages/dolfin/cpp/common.py in <module>()
     23         except ImportError:
     24             return importlib.import_module('_common')
---> 25     _common = swig_import_helper()
     26     del swig_import_helper
     27 elif _swig_python_version_info >= (2, 6, 0):

/home/rskolasinski/miniconda3/envs/fenics/lib/python2.7/site-packages/dolfin/cpp/common.py in swig_import_helper()
     22             return importlib.import_module(mname)
     23         except ImportError:
---> 24             return importlib.import_module('_common')
     25     _common = swig_import_helper()
     26     del swig_import_helper

/home/rskolasinski/miniconda3/envs/fenics/lib/python2.7/importlib/__init__.pyc in import_module(name, package)
     35             level += 1
     36         name = _resolve_name(name[level:], package, level)
---> 37     __import__(name)
     38     return sys.modules[name]

ImportError: No module named _common

ModuleNotFoundError: No module named '_common'

Maybe similar to #15 & #21
I am trying to install fenics from Anaconda on Linux:

4.10.13-1-ARCH #1 SMP PREEMPT Thu Apr 27 12:15:09 CEST 2017 x86_64 GNU/Linux

I am using miniconda3, python=3.6.1, conda=4.3.21

I created an environment and installed with:

conda create -n fenicsproject -c conda-forge fenics

fenics=2017.1.0 is succesfully installed, but when running: import fenics

I get the following error:

    return importlib.import_module(mname)
  File "/home/lbluque/.conda/envs/fenicsproject/lib/python3.6/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 978, in _gcd_import
  File "<frozen importlib._bootstrap>", line 961, in _find_and_load
  File "<frozen importlib._bootstrap>", line 950, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 648, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 560, in module_from_spec
  File "<frozen importlib._bootstrap_external>", line 922, in create_module
  File "<frozen importlib._bootstrap>", line 205, in _call_with_frames_removed
ImportError: /home/lbluque/.conda/envs/fenicsproject/bin/../lib/libstdc++.so.6: version 'CXXABI_1.3.8' not found (required by /usr/local/lib/python3.6/site-packages/dolfin/cpp/_common.so)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/lib/python3.6/site-packages/fenics/__init__.py", line 7, in <module>
    from dolfin import *
  File "/usr/local/lib/python3.6/site-packages/dolfin/__init__.py", line 17, in <module>
    from . import cpp
  File "/usr/local/lib/python3.6/site-packages/dolfin/cpp/__init__.py", line 43, in <module>
    exec("from . import %s" % module_name)
  File "<string>", line 1, in <module>
  File "/usr/local/lib/python3.6/site-packages/dolfin/cpp/common.py", line 21, in <module>
    _common = swig_import_helper()
  File "/usr/local/lib/python3.6/site-packages/dolfin/cpp/common.py", line 20, in swig_import_helper
    return importlib.import_module('_common')
  File "/home/lbluque/.conda/envs/fenicsproject/lib/python3.6/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)```

I have libgcc=5.2.0 installed in my environment.

Fails compilation on MacOS

I have installed fenics in the Mac Os X using conda-forge,
installed went normally, but the demo example fails (run from a jupyter notebook).
https://fenicsproject.org/documentation/dolfin/dev/python/demo/documented/auto-adaptive-poisson/python/documentation.html

It fails:

Calling FFC just-in-time (JIT) compiler, this may take some time.
--- Instant: compiling ---
In instant.recompile: The module did not compile with command 'make VERBOSE=1', see '/Users/ivan/miniconda2/envs/fenics/.cache/instant/error/dolfin_9413711742539ae5979228b94710829312b55df8/compile.log'

compile.txt

Fatal error in MPI_Init_thread: Other MPI error, error stack:

I've installed FEniCS through Anaconda on Mac OS X 10.12. When trying to run the first tutorial script I encounter the following error.

(fenicsproject) $ python ft01_poisson.py
Fatal error in MPI_Init_thread: Other MPI error, error stack:
MPIR_Init_thread(474)..............:
MPID_Init(190).....................: channel initialization failed
MPIDI_CH3_Init(89).................:
MPID_nem_init(320).................:
MPID_nem_tcp_init(173).............:
MPID_nem_tcp_get_business_card(420):
MPID_nem_tcp_init(379).............: gethostbyname failed, cylon.local (errno 1)
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=3191311
:
system msg for write_line failure : Bad file descriptor

Problem was solved by Johannes Ring:

"I have tested this on macOS 10.12 with both Python 2 and Python 3, and
they both works fine for me. I used this command to install:

conda create -n fenicsproject-py36 -c conda-forge fenics python=3.6
source activate fenicsproject-py36

Does this give you the same problem? If so, then please report the
issue at https://github.com/conda-forge/fenics-feedstock/issues. "

version `GLIBCXX_3.4.21' not found (required by /lib64/libboost_timer.so.1.64.0);

System: Fedora 27
Installation method: Anaconda

The error arises when running any FEniCS python sample file.

Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
--- Instant: compiling ---
In instant.import_module_directly: Failed to import module 'dolfin_dc17a5b57a6ee029129b3fd1d8b0dac5cc49a70b' from '/tmp/instant/cache/dolfin_dc17a5b57a6ee029129b3fd1d8b0dac5cc49a70b';
ImportError:/home/user/anaconda3/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/cpp/../../../../libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /lib64/libboost_timer.so.1.64.0);
Failed to import module found in cache. Modulename: 'dolfin_dc17a5b57a6ee029129b3fd1d8b0dac5cc49a70b';
Path: '/tmp/instant/cache/dolfin_dc17a5b57a6ee029129b3fd1d8b0dac5cc49a70b';
ImportError:/home/user/anaconda3/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/cpp/../../../../libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /lib64/libboost_timer.so.1.64.0);
Traceback (most recent call last):
  File "test_fenics.py", line 20, in <module>
    u_D = Expression('1 + x[0]*x[0] + 2*x[1]*x[1]', degree=2)
  File "/home/user/anaconda3/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/functions/expression.py", line 679, in __new__
    mpi_comm=kwargs.get("mpi_comm"))
  File "/home/user/anaconda3/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/compilemodules/expressions.py", line 266, in compile_expressions
    mpi_comm=mpi_comm)
  File "/home/user/anaconda3/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/compilemodules/expressions.py", line 183, in compile_expression_code
    mpi_comm=mpi_comm)
  File "/home/user/anaconda3/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/compilemodules/jit.py", line 70, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/home/user/anaconda3/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/compilemodules/compilemodule.py", line 603, in compile_extension_module
    **instant_kwargs)
  File "/home/user/anaconda3/envs/fenicsproject-py36/lib/python3.6/site-packages/instant/build.py", line 586, in build_module
    module = import_and_cache_module(module_path, modulename, moduleids)
  File "/home/user/anaconda3/envs/fenicsproject-py36/lib/python3.6/site-packages/instant/cache.py", line 92, in import_and_cache_module
    e))
  File "/home/user/anaconda3/envs/fenicsproject-py36/lib/python3.6/site-packages/instant/output.py", line 103, in instant_assert
    raise AssertionError(text)
AssertionError: Failed to import module found in cache. Modulename: 'dolfin_dc17a5b57a6ee029129b3fd1d8b0dac5cc49a70b';
Path: '/tmp/instant/cache/dolfin_dc17a5b57a6ee029129b3fd1d8b0dac5cc49a70b';
ImportError:/home/user/anaconda3/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/cpp/../../../../libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /lib64/libboost_timer.so.1.64.0);
Aborted (core dumped)

Installation of FEniCS via conda fails, because of missing shared libraries for MUMPS-MPI

Issue:
When installing FEniCS via conda, it pulls the package mumps-mpi, version 5.1.2, build blas_openblash08140c7_1001 [blas_openblas].
This package of mumps, however, does not contain shared libraries, but only static ones.

Trying to import dolfin consequently results in the following error
ImportError: libdmumps-5.1.2.so: cannot open shared object file: No such file or directory

Environment (conda list):

$ conda list
# 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_7  
blas                      1.1                    openblas    conda-forge
boost-cpp                 1.70.0               ha2d47e9_0    conda-forge
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
certifi                   2019.6.16                py37_0    conda-forge
cmake                     3.14.5               hf94ab9c_0    conda-forge
curl                      7.64.1               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_3    conda-forge
fenics-dijitso            2019.1.0                   py_3    conda-forge
fenics-dolfin             2019.1.0         py37h80b64ce_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             h9041177_3    conda-forge
fenics-ufl                2019.1.0                   py_3    conda-forge
gcc_impl_linux-64         7.3.0                habb00fd_1    conda-forge
gcc_linux-64              7.3.0                h553295d_7    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_7    conda-forge
hdf5                      1.10.4          mpi_mpich_ha7d0aea_1006    conda-forge
hypre                     2.15.1            hc98498a_1001    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
krb5                      1.16.3            h05b26f9_1001    conda-forge
libblas                   3.8.0           5_h6e990d7_netlib    conda-forge
libcblas                  3.8.0           5_h6e990d7_netlib    conda-forge
libcurl                   7.64.1               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           5_h6e990d7_netlib    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_1012    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
mumps-mpi                 5.1.2           blas_openblash08140c7_1001  [blas_openblas]  conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
numpy                     1.15.4          py37_blas_openblash1522bff_1000  [blas_openblas]  conda-forge
openblas                  0.3.3             h9ac9557_1001    conda-forge
openssl                   1.1.1b               h14c3975_1    conda-forge
parmetis                  4.0.3             hb1a587f_1002    conda-forge
petsc                     3.11.1               h624fa55_1    conda-forge
petsc4py                  3.11.0           py37h906564f_0    conda-forge
pip                       19.1.1                   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                     3.11.1               h00d104f_0    conda-forge
slepc4py                  3.11.0           py37hce3d510_0    conda-forge
sqlite                    3.28.0               hcee41ef_1    conda-forge
suitesparse               4.5.6           blas_openblash17e8c26_1201  [blas_openblas]  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            h14c3975_1004    conda-forge

Details about conda and system ( conda info ):

System 1: CentOS 7.5.1804

$ conda info
     active environment : fenics
    active env location : /home/hoelzlw/miniconda3/envs/fenics
            shell level : 2
       user config file : /home/hoelzlw/.condarc
 populated config files : /home/hoelzlw/.condarc
          conda version : 4.7.5
    conda-build version : not installed
         python version : 3.7.3.final.0
       virtual packages :
       base environment : /home/hoelzlw/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/hoelzlw/miniconda3/pkgs
                          /home/hoelzlw/.conda/pkgs
       envs directories : /home/hoelzlw/miniconda3/envs
                          /home/hoelzlw/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.5 requests/2.21.0 CPython/3.7.3 Linux/3.10.0-862.3.3.el7.x86_64 centos/7.5.1804 glibc/2.17
                UID:GID : 1302:200
             netrc file : None
           offline mode : False

System 2: Windows 10 1809, WSL Ubuntu 18.04

$ conda info
     active environment : FEniCS
    active env location : /home/hoelzlw/miniconda3/envs/FEniCS
            shell level : 3
       user config file : /home/hoelzlw/.condarc
 populated config files : /home/hoelzlw/.condarc
          conda version : 4.7.5
    conda-build version : not installed
         python version : 3.7.3.final.0
       virtual packages :
       base environment : /home/hoelzlw/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/hoelzlw/miniconda3/pkgs
                          /home/hoelzlw/.conda/pkgs
       envs directories : /home/hoelzlw/miniconda3/envs
                          /home/hoelzlw/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.5 requests/2.21.0 CPython/3.7.3 Linux/4.4.0-17763-Microsoft ubuntu/18.04.2 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Steps to reproduce:

Install miniconda:

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash ./Miniconda3-latest-Linux-x86_64.sh -b
./miniconda3/bin/conda update -n base conda

Create environment for FEniCS:

./miniconda3/bin/conda create --name fenics
./miniconda3/bin/conda activate fenics

Install FEniCS

conda install -c conda-forge fenics

Try to import dolfin

python -c "from dolfin import *"

Error message:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/hoelzlw/miniconda3/envs/fenics/lib/python3.7/site-packages/dolfin/__init__.py", line 34, in <module>
    from .cpp import __version__
ImportError: libdmumps-5.1.2.so: cannot open shared object file: No such file or directory

There are other conda packages of MUMPS-MPI which contain shared libraries, but none of these can be installed into the FEniCS-environment because the specifications are found to be incompatible with each other.

Best regards
Wolfgang

FEniCS conda Mac OS X questions

Hello, I've installed FEniCS via conda on Mac OS X Sierra, and am able to import dolfin. I have a few questions:

1. Is mshr available on the FEniCS conda package? I get the error 'no module named mshr' when I try to import mshr.

2. I also get an error 'name TimeSeries is not defined'. Is there anyway to fix this?

3. What is the best way to run a FEniCS script in Anaconda? I'm using Spyder, but am not able to obtain any plots. I don't get any errors when I try to plot, I just don't see any plots.

4. I installed Anaconda navigator (graphical installer), and it was working fine, but after installing FEniCS, (which downgraded Anaconda from 1.4 to 1.2), the Navigator does not work anymore.

Thank you

Fails to import correctly on RedHat Linux

Tried installing on our compute cluster at the University of Southampton, installs fine but when trying to import in Python

>>> import fenics
Traceback (most recent call last):
  File "/scratch/rp20g15/anaconda/envs/py35/lib/python3.5/site-packages/dolfin/cpp/common.py", line 18, in swig_import_helper
    return importlib.import_module(mname)
  File "/scratch/rp20g15/anaconda/envs/py35/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 986, in _gcd_import
  File "<frozen importlib._bootstrap>", line 969, in _find_and_load
  File "<frozen importlib._bootstrap>", line 958, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 666, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 577, in module_from_spec
  File "<frozen importlib._bootstrap_external>", line 906, in create_module
  File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
ImportError: libumfpack.so.5: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/scratch/rp20g15/anaconda/envs/py35/lib/python3.5/site-packages/fenics/__init__.py", line 7, in <module>
    from dolfin import *
  File "/scratch/rp20g15/anaconda/envs/py35/lib/python3.5/site-packages/dolfin/__init__.py", line 17, in <module>
    from . import cpp
  File "/scratch/rp20g15/anaconda/envs/py35/lib/python3.5/site-packages/dolfin/cpp/__init__.py", line 43, in <module>
    exec("from . import %s" % module_name)
  File "<string>", line 1, in <module>
  File "/scratch/rp20g15/anaconda/envs/py35/lib/python3.5/site-packages/dolfin/cpp/common.py", line 21, in <module>
    _common = swig_import_helper()
  File "/scratch/rp20g15/anaconda/envs/py35/lib/python3.5/site-packages/dolfin/cpp/common.py", line 20, in swig_import_helper
    return importlib.import_module('_common')
  File "/scratch/rp20g15/anaconda/envs/py35/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ImportError: No module named '_common'

multiple outputs versus the build matrix

I'd love some advice on best practices

While "fenics" is one project, it's actually several packages with coordinated releases and strict exact-version compatibility:

• ffc, ufl, dijitso, fiat (noarch Python packages)
• libdolfin (C++, requires ffc at buildtime)
• dolfin (compiled Python package, and the main thing folks use directly)
• fenics (metapackage)

Until recently, fenics was a single conda package with all of this put together. However, now each of these packages is a separate conda package, produced as an output in this recipe. This is where things get hairy! Splitting into multiple outputs has significant promise in reducing redundancy, but it results in loads of unnecessary rebuilds: the noarch Python packages and libdolfin do not need to be rebuilt for new Python releases, only dolfin does. However, because of that, we don't get multiple entries in the azure build matrix, we only get multiple builds of dolfin. So we get wasted rebuilds (rebuilding several noarch packages costs a nontrivial amount of time) and also get slower rebuilds because we lose the parallelism of the build matrix.

So my question is: what's the best strategy going forward?

• stick with what we have now, which is inefficient (unnecessary rebuilds and uploads of unchanged packages)
• separate noarch packages into their own recipe (or one recipe per Python package, which would make coordinated releases take a very long time as we wait for PR build / merge build / CDN upload)
• in addition to separate noarch packages, separate dolfin from libdolfin to get the Python build matrix parallelism back

Azure Notebook: ModuleNotFoundError: No module named '_common

The ModuleNotFoundError: No module named '_common error has been reported several times. Still, I have found no way to run fenics locally. I tried remotely with Azure Notebooks (Python 3.6). Still no luck.

My Azure Notebook

Cell input

!conda config --add channels conda-forge
!conda install fenics -y
from fenics import *

Cell output

Fetching package metadata ...........
Solving package specifications: .

Package plan for installation in environment /home/nbcommon/anaconda3_431:

The following NEW packages will be INSTALLED:

    boost:       1.64.0-py36_4           conda-forge
    boost-cpp:   1.64.0-1                conda-forge
    cloog:       0.18.0-0                           
    cmake:       3.9.1-0                 conda-forge
    eigen:       3.3.3-0                 conda-forge
    fenics:      2017.1.0-py36_5         conda-forge
    gcc:         4.8.5-7                            
    gmp:         6.1.2-0                 conda-forge
    isl:         0.12.2-0                           
    libuv:       1.11.0-0                conda-forge
    metis:       5.1.0-3                 conda-forge
    mpc:         1.0.3-4                 conda-forge
    mpfr:        3.1.5-0                 conda-forge
    mpich:       3.2-4                   conda-forge
    ncurses:     5.9-10                  conda-forge
    petsc:       3.7.6-blas_openblas_0   conda-forge [blas_openblas]
    petsc4py:    3.7.0-py36_1            conda-forge
    pkg-config:  0.29.1-1                conda-forge
    ptscotch:    6.0.4-2                 conda-forge
    rhash:       1.3.4-0                 conda-forge
    slepc:       3.7.4-0                 conda-forge
    slepc4py:    3.7.0-py36_0            conda-forge
    suitesparse: 4.5.4-blas_openblas_200 conda-forge [blas_openblas]
    swig:        3.0.12-2                conda-forge
    tbb:         2017_20170604-1         conda-forge

The following packages will be SUPERSEDED by a higher-priority channel:

    conda:       4.3.24-py36_0                       --> 4.3.23-py36_0 conda-forge
    conda-env:   2.6.0-0                             --> 2.6.0-0       conda-forge

conda-env-2.6. 100% |################################| Time: 0:00:00   1.24 MB/s
eigen-3.3.3-0. 100% |################################| Time: 0:00:00   2.53 MB/s
gmp-6.1.2-0.ta 100% |################################| Time: 0:00:00   9.83 MB/s
libuv-1.11.0-0 100% |################################| Time: 0:00:00   7.53 MB/s
metis-5.1.0-3. 100% |################################| Time: 0:00:00   6.97 MB/s
ncurses-5.9-10 100% |################################| Time: 0:00:00  10.40 MB/s
rhash-1.3.4-0. 100% |################################| Time: 0:00:00 708.10 kB/s
tbb-2017_20170 100% |################################| Time: 0:00:00  11.91 MB/s
boost-cpp-1.64 100% |################################| Time: 0:00:00  44.05 MB/s
isl-0.12.2-0.t 100% |################################| Time: 0:00:00   6.07 MB/s
mpfr-3.1.5-0.t 100% |################################| Time: 0:00:00  52.04 MB/s
mpich-3.2-4.ta 100% |################################| Time: 0:00:00  19.45 MB/s
pkg-config-0.2 100% |################################| Time: 0:00:00  47.12 MB/s
cloog-0.18.0-0 100% |################################| Time: 0:00:00  10.80 MB/s
cmake-3.9.1-0. 100% |################################| Time: 0:00:00  22.09 MB/s
mpc-1.0.3-4.ta 100% |################################| Time: 0:00:00  40.24 MB/s
ptscotch-6.0.4 100% |################################| Time: 0:00:00  32.91 MB/s
swig-3.0.12-2. 100% |################################| Time: 0:00:00  31.24 MB/s
gcc-4.8.5-7.ta 100% |################################| Time: 0:00:01  45.55 MB/s
suitesparse-4. 100% |################################| Time: 0:00:00   2.27 MB/s
boost-1.64.0-p 100% |################################| Time: 0:00:00   3.21 MB/s
petsc-3.7.6-bl 100% |################################| Time: 0:00:00   6.49 MB/s
petsc4py-3.7.0 100% |################################| Time: 0:00:00   9.13 MB/s
slepc-3.7.4-0. 100% |################################| Time: 0:00:00   8.33 MB/s
slepc4py-3.7.0 100% |################################| Time: 0:00:00  12.96 MB/s
fenics-2017.1. 100% |################################| Time: 0:00:01  32.13 MB/s
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
~/anaconda3_431/lib/python3.6/site-packages/dolfin/cpp/common.py in swig_import_helper()
     17         try:
---> 18             return importlib.import_module(mname)
     19         except ImportError:

~/anaconda3_431/lib/python3.6/importlib/__init__.py in import_module(name, package)
    125             level += 1
--> 126     return _bootstrap._gcd_import(name[level:], package, level)
    127 

~/anaconda3_431/lib/python3.6/importlib/_bootstrap.py in _gcd_import(name, package, level)

~/anaconda3_431/lib/python3.6/importlib/_bootstrap.py in _find_and_load(name, import_)

~/anaconda3_431/lib/python3.6/importlib/_bootstrap.py in _find_and_load_unlocked(name, import_)

~/anaconda3_431/lib/python3.6/importlib/_bootstrap.py in _load_unlocked(spec)

~/anaconda3_431/lib/python3.6/importlib/_bootstrap.py in module_from_spec(spec)

~/anaconda3_431/lib/python3.6/importlib/_bootstrap_external.py in create_module(self, spec)

~/anaconda3_431/lib/python3.6/importlib/_bootstrap.py in _call_with_frames_removed(f, *args, **kwds)

ImportError: numpy.core.multiarray failed to import

During handling of the above exception, another exception occurred:

ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-1-31dd07c0e296> in <module>()
      1 get_ipython().system('conda config --add channels conda-forge')
      2 get_ipython().system('conda install fenics -y')
----> 3 from fenics import *

~/anaconda3_431/lib/python3.6/site-packages/fenics/__init__.py in <module>()
      5 """
      6 
----> 7 from dolfin import *

~/anaconda3_431/lib/python3.6/site-packages/dolfin/__init__.py in <module>()
     15 
     16 # Import names from the compiled cpp modules
---> 17 from . import cpp
     18 from dolfin.cpp import *
     19 from dolfin.cpp import __version__, __swigversion__, __pythonversion__

~/anaconda3_431/lib/python3.6/site-packages/dolfin/cpp/__init__.py in <module>()
     41 
     42     # Import the module
---> 43     exec("from . import %s" % module_name)
     44     module = globals()[module_name]
     45 

~/anaconda3_431/lib/python3.6/site-packages/dolfin/cpp/__init__.py in <module>()

~/anaconda3_431/lib/python3.6/site-packages/dolfin/cpp/common.py in <module>()
     19         except ImportError:
     20             return importlib.import_module('_common')
---> 21     _common = swig_import_helper()
     22     del swig_import_helper
     23 elif _swig_python_version_info >= (2, 6, 0):

~/anaconda3_431/lib/python3.6/site-packages/dolfin/cpp/common.py in swig_import_helper()
     18             return importlib.import_module(mname)
     19         except ImportError:
---> 20             return importlib.import_module('_common')
     21     _common = swig_import_helper()
     22     del swig_import_helper

~/anaconda3_431/lib/python3.6/importlib/__init__.py in import_module(name, package)
    124                 break
    125             level += 1
--> 126     return _bootstrap._gcd_import(name[level:], package, level)
    127 
    128 

ModuleNotFoundError: No module named '_common

Cannot use superlu or superlu_dist solvers

Issue: Cannot use superlu or superlu_dist solvers

I am trying to solve a problem that requires the use of superlu_dist but it does not seem to be configured with PETSc inside my environment. I see however that superlu/5.2.1 and superlu_dist/6.2.0 are installed in the current finics package ($ conda install -c conda-forge fenics), but they do not appear as available methods.

Here is the output:

>>> list_linear_solver_methods()
Solver method  |  Description
------------------------------------------------------------------------------
bicgstab      |  Biconjugate gradient stabilized method
cg               |  Conjugate gradient method
default        |  default linear solver
gmres          |  Generalized minimal residual method
minres         |  Minimal residual method
mumps          |  MUMPS (MUltifrontal Massively Parallel Sparse direct Solver)
petsc          |  PETSc built in LU solver
richardson     |  Richardson method
tfqmr          |  Transpose-free quasi-minimal residual method
umfpack        |  UMFPACK (Unsymmetric MultiFrontal sparse LU factorization)

>>> list_lu_solver_methods()
LU method  |  Description
--------------------------------------------------------------------------
default    |  default LU solver
mumps      |  MUMPS (MUltifrontal Massively Parallel Sparse direct Solver)
petsc      |  PETSc built in LU solver
umfpack    |  UMFPACK (Unsymmetric MultiFrontal sparse LU factorization)

Any help is appreciated!

Errors after installing FEniCS

Hello, this issue has been raised before, i looked through the previous posts, but could not figure out the solution. I tried installing a previous verison of fenics, and that did not work, and installed the latest version again, and i get the following error,

from fenics import *

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/fenics/__init__.py", line 7, in <module>

    from dolfin import *

  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/dolfin/__init__.py", line 17, in <module>

    from . import cpp

  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/dolfin/cpp/__init__.py", line 43, in <module>

    exec("from . import %s" % module_name)

  File "<string>", line 1, in <module>

  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/dolfin/cpp/common.py", line 21, in <module>

    _common = swig_import_helper()

  File "/Users/sophiaw/anaconda/lib/python2.7/site-packages/dolfin/cpp/common.py", line 20, in swig_import_helper

    return importlib.import_module('_common')

  File "/Users/sophiaw/anaconda/lib/python2.7/importlib/__init__.py", line 37, in import_module

    __import__(name)

ImportError: No module named _common

Any help to fix this would be greatly appreciated - Thank you.

Can't use fenics from conda

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Hi,
I'm trying to install fenics via conda since I need a newer version of python.

I'm using the continuumio/miniconda3 docker image to install fenics via:

conda install -c conda-forge fenics

Everything works fine on my windows machine, but when running on ubuntu it seems that the c++ files are not found:

Traceback (most recent call last):
  File "/__w/FESTIM-workshop/FESTIM-workshop/tasks/task1.py", line 74, in <module>
    my_model.initialise()
  File "/opt/conda/lib/python3.9/site-packages/festim/generic_simulation.py", line 237, in initialise
    self.V_DG1 = FunctionSpace(self.mesh.mesh, "DG", 1)
  File "/opt/conda/lib/python3.9/site-packages/dolfin/function/functionspace.py", line 33, in __init__
    self._init_convenience(*args, **kwargs)
  File "/opt/conda/lib/python3.9/site-packages/dolfin/function/functionspace.py", line 100, in _init_convenience
    self._init_from_ufl(mesh, element, constrained_domain=constrained_domain)
  File "/opt/conda/lib/python3.9/site-packages/dolfin/function/functionspace.py", line 42, in _init_from_ufl
    ufc_element, ufc_dofmap = ffc_jit(element, form_compiler_parameters=None,
  File "/opt/conda/lib/python3.9/site-packages/dolfin/jit/jit.py", line 47, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/opt/conda/lib/python3.9/site-packages/dolfin/jit/jit.py", line 97, in ffc_jit
    return ffc.jit(ufl_form, parameters=p)
  File "/opt/conda/lib/python3.9/site-packages/ffc/jitcompiler.py", line 217, in jit
    module = jit_build(ufl_object, module_name, parameters)
  File "/opt/conda/lib/python3.9/site-packages/ffc/jitcompiler.py", line [13](https://github.com/RemDelaporteMathurin/FESTIM-workshop/runs/7743762381?check_suite_focus=true#step:6:14)0, in jit_build
    module, signature = dijitso.jit(jitable=ufl_object,
  File "/opt/conda/lib/python3.9/site-packages/dijitso/jit.py", line 177, in jit
    build_shared_library(signature, header, source, dependencies,
  File "/opt/conda/lib/python3.9/site-packages/dijitso/build.py", line [15](https://github.com/RemDelaporteMathurin/FESTIM-workshop/runs/7743762381?check_suite_focus=true#step:6:16)3, in build_shared_library
    status, output = get_status_output(cmd)
  File "/opt/conda/lib/python3.9/site-packages/dijitso/system.py", line 40, in _get_status_output_subprocess
    pipe = subprocess.Popen(cmd, shell=False, cwd=cwd, env=env,
  File "/opt/conda/lib/python3.9/subprocess.py", line 951, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/opt/conda/lib/python3.9/subprocess.py", line [18](https://github.com/RemDelaporteMathurin/FESTIM-workshop/runs/7743762381?check_suite_focus=true#step:6:19)[21](https://github.com/RemDelaporteMathurin/FESTIM-workshop/runs/7743762381?check_suite_focus=true#step:6:22), in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'c++'

Full error message here

Here is the github actions file.

Installed packages

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             4.5                       1_gnu  
attrs                     22.1.0                   pypi_0    pypi
beautifulsoup4            4.11.1                   pypi_0    pypi
binutils_impl_linux-64    2.35.1               h27ae35d_9  
binutils_linux-64         2.35                h67ddf6f_30    conda-forge
bleach                    5.0.1                    pypi_0    pypi
boost-cpp                 1.74.0               h312852a_4    conda-forge
brotlipy                  0.7.0           py39h27cfd23_1003  
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h7f98852_1    conda-forge
ca-certificates           2022.6.15            ha878542_0    conda-forge
certifi                   2022.6.15        py39hf3d152e_0    conda-forge
cffi                      1.15.0           py39hd667e15_1  
cftime                    1.6.1                    pypi_0    pypi
charset-normalizer        2.0.4              pyhd3eb1b0_0  
cmake                     3.21.1               h8897547_0    conda-forge
colorama                  0.4.4              pyhd3eb1b0_0  
commonmark                0.9.1                    pypi_0    pypi
conda                     4.13.0           py39hf3d152e_1    conda-forge
conda-content-trust       0.1.1              pyhd3eb1b0_0  
conda-package-handling    1.8.1            py39h7f8727e_0  
crossrefapi               1.5.0                    pypi_0    pypi
cryptography              36.0.0           py39h9ce1e76_0  
cycler                    0.11.0                   pypi_0    pypi
defusedxml                0.7.1                    pypi_0    pypi
eigen                     3.3.9                h4bd325d_1    conda-forge
entrypoints               0.4                      pypi_0    pypi
expat                     2.4.1                h9c3ff4c_0    conda-forge
fastjsonschema            2.16.1                   pypi_0    pypi
fenics                    2019.1.0        py39hf3d152e_21    conda-forge
fenics-dijitso            2019.1.0        py39hf3d152e_21    conda-forge
fenics-dolfin             2019.1.0        py39hc6fefde_21    conda-forge
fenics-ffc                2019.1.0        py39hf3d152e_21    conda-forge
fenics-fiat               2019.1.0        py39hf3d152e_21    conda-forge
fenics-libdolfin          2019.1.0            h5ba192a_21    conda-forge
fenics-ufl                2019.1.0        py39hf3d152e_21    conda-forge
festim                    0.10.2                   pypi_0    pypi
fonttools                 4.34.4                   pypi_0    pypi
gcc_impl_linux-64         9.3.0               h70c0ae5_19    conda-forge
gcc_linux-64              9.3.0               hf25ea35_30    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmpy2                     2.1.0b5          py39h78fa15d_0    conda-forge
gxx_impl_linux-64         9.3.0               hd87eabc_19    conda-forge
gxx_linux-64              9.3.0               h3fbe746_30    conda-forge
h-transport-materials     0.4.0                    pypi_0    pypi
h5py                      3.7.0                    pypi_0    pypi
hdf5                      1.10.6          mpi_mpich_h996c276_1014    conda-forge
hypre                     2.18.2               hc98498a_1    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
idna                      3.3                pyhd3eb1b0_0  
jinja2                    3.1.2                    pypi_0    pypi
jsonschema                4.9.1                    pypi_0    pypi
jupyter-client            7.3.4                    pypi_0    pypi
jupyter-core              4.11.1                   pypi_0    pypi
jupyterlab-pygments       0.2.2                    pypi_0    pypi
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
kiwisolver                1.4.4                    pypi_0    pypi
krb5                      1.19.2               hcc1bbae_0    conda-forge
latexcodec                2.0.1                    pypi_0    pypi
ld_impl_linux-64          2.35.1               h7274673_9  
libblas                   3.9.0           11_linux64_openblas    conda-forge
libcblas                  3.9.0           11_linux64_openblas    conda-forge
libcurl                   7.78.0               h2574ce0_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.3                  he6710b0_2  
libgcc-devel_linux-64     9.3.0               h7864c58_19    conda-forge
libgcc-ng                 9.3.0               h5101ec6_17  
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
libgomp                   9.3.0               h5101ec6_17  
liblapack                 3.9.0           11_linux64_openblas    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libopenblas               0.3.17          pthreads_h8fe5266_1    conda-forge
libssh2                   1.9.0                ha56f1ee_6    conda-forge
libstdcxx-devel_linux-64  9.3.0               hb016644_19    conda-forge
libstdcxx-ng              9.3.0               hd4cf53a_17  
libuv                     1.42.0               h7f98852_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
markupsafe                2.1.1                    pypi_0    pypi
matplotlib                3.5.2                    pypi_0    pypi
meshio                    5.3.4                    pypi_0    pypi
metis                     5.1.0             h58526e2_1006    conda-forge
mistune                   0.8.4                    pypi_0    pypi
mpc                       1.2.1                h9f54685_0    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
mpi                       1.0                       mpich    conda-forge
mpi4py                    3.0.3            py39h6438238_7    conda-forge
mpich                     3.4.2              h846660c_100    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
mumps-include             5.2.1               ha770c72_10    conda-forge
mumps-mpi                 5.2.1               hd6b9cac_10    conda-forge
nbclient                  0.6.6                    pypi_0    pypi
nbconvert                 6.5.0                    pypi_0    pypi
nbformat                  5.4.0                    pypi_0    pypi
ncurses                   6.3                  h7f8727e_2  
nest-asyncio              1.5.5                    pypi_0    pypi
netcdf4                   1.6.0                    pypi_0    pypi
numpy                     1.21.1           py39hdbf815f_0    conda-forge
openssl                   1.1.1q               h7f8727e_0  
packaging                 21.3                     pypi_0    pypi
pandocfilters             1.5.0                    pypi_0    pypi
parmetis                  4.0.3             h2a9763c_1005    conda-forge
petsc                     3.14.5               h60475ce_0    conda-forge
petsc4py                  3.14.1           py39h16c3f58_1    conda-forge
pillow                    9.2.0                    pypi_0    pypi
pip                       22.2.2                   pypi_0    pypi
pkg-config                0.29.2            h36c2ea0_1008    conda-forge
pkgconfig                 1.5.5            py39hf3d152e_2    conda-forge
ptscotch                  6.0.9                h253636d_1    conda-forge
pybind11                  2.6.2            py39h1a9c180_0    conda-forge
pybind11-global           2.6.2            py39h1a9c180_0    conda-forge
pybtex                    0.24.0                   pypi_0    pypi
pycosat                   0.6.3            py39h27cfd23_0  
pycparser                 2.21               pyhd3eb1b0_0  
pygments                  2.12.0                   pypi_0    pypi
pyopenssl                 22.0.0             pyhd3eb1b0_0  
pyparsing                 3.0.9                    pypi_0    pypi
pyrsistent                0.18.1                   pypi_0    pypi
pysocks                   1.7.1            py39h06a4308_0  
python                    3.9.12               h12debd9_0  
python-dateutil           2.8.2                    pypi_0    pypi
python_abi                3.9                      2_cp39    conda-forge
pyyaml                    6.0                      pypi_0    pypi
pyzmq                     23.2.0                   pypi_0    pypi
readline                  8.1.2                h7f8727e_1  
requests                  2.27.1             pyhd3eb1b0_0  
rhash                     1.4.1                h7f98852_0    conda-forge
rich                      12.5.1                   pypi_0    pypi
ruamel_yaml               0.15.100         py39h27cfd23_0  
scalapack                 2.0.2             hf659fdc_1009    conda-forge
scipy                     1.9.0                    pypi_0    pypi
scotch                    6.0.9                h3858553_1    conda-forge
setuptools                61.2.0           py39h06a4308_0  
six                       1.16.0             pyhd3eb1b0_1  
slepc                     3.14.2               h44d3fa2_0    conda-forge
slepc4py                  3.14.0           py39h1e75aa9_1    conda-forge
soupsieve                 2.3.2.post1              pypi_0    pypi
sqlite                    3.38.2               hc218d9a_0  
suitesparse               5.6.0                h717dc36_0    conda-forge
superlu                   5.2.2                h16cfea0_0    conda-forge
superlu_dist              6.2.0                h25dcc4a_4    conda-forge
sympy                     1.10.1           py39hf3d152e_0    conda-forge
sysroot_linux-64          2.12                he073ed8_15    conda-forge
tbb                       2020.2               h4bd325d_4    conda-forge
tinycss2                  1.1.1                    pypi_0    pypi
tk                        8.6.11               h1ccaba5_0  
tornado                   6.2                      pypi_0    pypi
tqdm                      4.63.0             pyhd3eb1b0_0  
traitlets                 5.3.0                    pypi_0    pypi
tzdata                    2022a                hda174b7_0  
urllib3                   1.26.8             pyhd3eb1b0_0  
webencodings              0.5.1                    pypi_0    pypi
wheel                     0.37.1             pyhd3eb1b0_0  
xz                        5.2.5                h7b6447c_0  
yaml                      0.2.5                h7b6447c_0  
zlib                      1.2.12               h7f8727e_1  
zstd                      1.5.0                ha95c52a_0    conda-forge

Environment info

active environment : None
       user config file : /github/home/.condarc
 populated config files : 
          conda version : 4.13.0
    conda-build version : not installed
         python version : 3.9.12.final.0
       virtual packages : __linux=5.15.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /opt/conda  (writable)
      conda av data dir : /opt/conda/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/conda/pkgs
                          /github/home/.conda/pkgs
       envs directories : /opt/conda/envs
                          /github/home/.conda/envs
               platform : linux-64
             user-agent : conda/4.13.0 requests/2.27.1 CPython/3.9.12 Linux/5.15.0-1014-azure debian/11 glibc/2.31
                UID:GID : 0:0
             netrc file : None
           offline mode : False

TypeError with PETScVector

Issue:

We get an TypeError concerning PETSc_exp, if we try to run a Dolfin unix test with fenics installed via anaconda. Has someone an idea how to fix this?
The Error reads:

(Rbnics) ~/.../programmieren/fenics/Rbnics$ python3 tmp.py 
Traceback (most recent call last):
  File "tmp.py", line 30, in <module>
    ext_module.PETSc_exp(vec)
TypeError: PETSc_exp(): incompatible function arguments. The following argument types are 
supported:
    1. (arg0: dolfin::PETScVector) -> None
Invoked with: <dolfin.cpp.la.PETScVector object at 0x7fd893ee8888>

The example file (tmp.py) looks like:

$ tmp.py

## Test taken from DOLFIN/python/test/unit/jit/test_jit.py ##

from dolfin import *
from numpy import arange, exp
code = """
  #include <pybind11/pybind11.h>

  #include <petscvec.h>
  #include <dolfin/la/PETScVector.h>

  void PETSc_exp(std::shared_ptr<dolfin::PETScVector> vec)
  {
    Vec x = vec->vec();
    assert(x);
    VecExp(x);
  }

PYBIND11_MODULE(SIGNATURE, m)
{
  m.def("PETSc_exp", &PETSc_exp);
}
"""

ext_module = compile_cpp_code(code)

vec = PETScVector(MPI.comm_world, 10)
np_vec = vec.get_local()
np_vec[:] = arange(len(np_vec))
vec.set_local(np_vec)
ext_module.PETSc_exp(vec)
np_vec[:] = exp(np_vec)
print(np_vec)
assert (np_vec == vec.get_local()).all()

Environment (conda list):

$ conda list
# packages in environment at /home/.../anaconda3/envs/Rbnics:
#
# Name                    Version                   Build  Channel
backcall                  0.1.0                      py_0    conda-forge
blas                      1.1                    openblas    conda-forge
boost                     1.67.0           py36h3e44d54_0    conda-forge
boost-cpp                 1.67.0               h3a22d5f_0    conda-forge
bzip2                     1.0.6                h470a237_2    conda-forge
ca-certificates           2018.8.24            ha4d7672_0    conda-forge
certifi                   2018.8.24                py36_1    conda-forge
cloog                     0.18.0                        0  
cmake                     3.12.2               h011004d_0    conda-forge
curl                      7.61.0               h93b3f91_2    conda-forge
cvxopt                    1.2.1                     <pip>
cycler                    0.10.0                     py_1    conda-forge
dbus                      1.13.0               h3a4f0e9_0    conda-forge
decorator                 4.3.0                      py_0    conda-forge
eigen                     3.3.5                h2d50403_1    conda-forge
expat                     2.2.5                hfc679d8_2    conda-forge
fastcache                 1.0.2            py36h470a237_1    conda-forge
fenics                    2018.1.0         py36hba71e3e_1    conda-forge
fontconfig                2.13.1               h65d0f4c_0    conda-forge
freetype                  2.9.1                h6debe1e_4    conda-forge
gcc                       4.8.5                         7  
gettext                   0.19.8.1             h5e8e0c9_1    conda-forge
glib                      2.55.0               h464dc38_2    conda-forge
gmp                       6.1.2                hfc679d8_0    conda-forge
gmpy2                     2.0.8                    py36_1    conda-forge
gst-plugins-base          1.12.5               hde13a9d_0    conda-forge
gstreamer                 1.12.5               h61a6719_0    conda-forge
hdf5                      1.10.2               hc401514_2    conda-forge
hypre                     2.14.0               h7df9f4f_1    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
ipython                   6.5.0                    py36_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
isl                       0.12.2                        0  
jedi                      0.12.1                   py36_0    conda-forge
jpeg                      9c                   h470a237_1    conda-forge
kiwisolver                1.0.1            py36h2d50403_2    conda-forge
krb5                      1.14.6                        0    conda-forge
libffi                    3.2.1                hfc679d8_5    conda-forge
libgcc-ng                 7.2.0                hdf63c60_3    conda-forge
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.2.0                hdf63c60_3    conda-forge
libiconv                  1.15                 h470a237_3    conda-forge
libpng                    1.6.35               ha92aebf_2    conda-forge
libssh2                   1.8.0                h5b517e9_2    conda-forge
libstdcxx-ng              7.2.0                hdf63c60_3    conda-forge
libuuid                   2.32.1               h470a237_2    conda-forge
libuv                     1.22.0               h470a237_1    conda-forge
libxcb                    1.13                 h470a237_2    conda-forge
libxml2                   2.9.8                h422b904_5    conda-forge
matplotlib                2.2.3            py36h8e2386c_0    conda-forge
metis                     5.1.0                h470a237_3    conda-forge
mpc                       1.1.0                         4    conda-forge
mpfr                      3.1.5                         0    conda-forge
mpi                       1.0                       mpich    conda-forge
mpi4py                    3.0.0              py36_mpich_3    conda-forge
mpich                     3.2.1                h26a2512_4    conda-forge
mpmath                    1.0.0                      py_0    conda-forge
mshr                      2018.1.0         py36h49bd758_0    conda-forge
multipledispatch          0.6.0                     <pip>
mumps-mpi                 5.1.2           blas_openblasha5050ec_0  [blas_openblas]  conda-forge
ncurses                   6.1                  hfc679d8_1    conda-forge
numpy                     1.14.5          py36_blas_openblashd3ea46f_202  [blas_openblas]  conda-forge
openblas                  0.2.20                        8    conda-forge
openssl                   1.0.2p               h470a237_0    conda-forge
parmetis                  4.0.3                hf0665dc_2    conda-forge
parso                     0.3.1                      py_0    conda-forge
pcre                      8.41                 hfc679d8_3    conda-forge
petsc                     3.9.4           blas_openblash330393b_0  [blas_openblas]  conda-forge
petsc4py                  3.9.1            py36h18b3941_1    conda-forge
pexpect                   4.6.0                    py36_0    conda-forge
pickleshare               0.7.4                    py36_0    conda-forge
pip                       18.0                     py36_1    conda-forge
pkg-config                0.29.2               h470a237_3    conda-forge
pkgconfig                 1.3.1                    py36_1    conda-forge
prompt_toolkit            1.0.15                     py_1    conda-forge
pthread-stubs             0.4                  h470a237_1    conda-forge
ptscotch                  6.0.5                ha5050ec_0    conda-forge
ptyprocess                0.6.0                    py36_0    conda-forge
pybind11                  2.2.4            py36h2d50403_1    conda-forge
pygments                  2.2.0                      py_1    conda-forge
pylru                     1.1.0                     <pip>
pyparsing                 2.2.1                      py_0    conda-forge
pyqt                      5.6.0            py36h8210e8a_7    conda-forge
pytest-runner             4.2                       <pip>
python                    3.6.6                h5001a0f_0    conda-forge
python-dateutil           2.7.3                      py_0    conda-forge
pytz                      2018.5                     py_0    conda-forge
qt                        5.6.2                hf70d934_9    conda-forge
RBniCS                    0.0.dev2                  <pip>
readline                  7.0                  haf1bffa_1    conda-forge
rhash                     1.3.4                         0    conda-forge
scalapack                 2.0.2                h186ce0b_3    conda-forge
scipy                     1.1.0                     <pip>
scotch                    6.0.5                h9c0d707_1    conda-forge
setuptools                40.4.0                   py36_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
sip                       4.18.1           py36hfc679d8_0    conda-forge
six                       1.11.0                   py36_1    conda-forge
slepc                     3.9.2           blas_openblashe63b0ae_0  [blas_openblas]  conda-forge
slepc4py                  3.9.0            py36h7eb728f_1    conda-forge
sqlite                    3.24.0               h2f33b56_1    conda-forge
suitesparse               4.5.6           blas_openblash55dcaef_201  [blas_openblas]  conda-forge
sympy                     1.1.1                    py36_0    conda-forge
tbb                       2018_20171205                 0    conda-forge
tk                        8.6.8                ha92aebf_0    conda-forge
toposort                  1.5                       <pip>
tornado                   5.1.1            py36h470a237_0    conda-forge
traitlets                 4.3.2                    py36_0    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
wheel                     0.31.1                   py36_1    conda-forge
xorg-libxau               1.0.8                h470a237_6    conda-forge
xorg-libxdmcp             1.1.2                h470a237_7    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

Details about conda and system ( conda info ):

$ conda info
     active environment : Rbnics
    active env location : /home/araderma/anaconda3/envs/Rbnics
            shell level : 1
       user config file : /home/araderma/.condarc
 populated config files : /home/araderma/.condarc
          conda version : 4.5.11
    conda-build version : 3.10.5
         python version : 3.6.5.final.0
       base environment : /home/araderma/anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /home/araderma/anaconda3/pkgs
                          /home/araderma/.conda/pkgs
       envs directories : /home/araderma/anaconda3/envs
                          /home/araderma/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.11 requests/2.18.4 CPython/3.6.5 Linux/4.17.0-1-amd64 debian/testing glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

@francesco-ballarin

petsc with hypre and ml

The fenics build is missing some preconditions based on hypre and ml. It seems that it is because petsc was not built with hypre and ml, leaving some important preconditions out. The docker image supports both. Would you please enable hypre and ml for petsc? Thanks!

ImportError: cannot import name HDF5File for Fenics

Hello I am trying to install fenics in Conda with python2.7. with following error. can anyone help?

Issue:
Traceback (most recent call last):
File "single_runner.py", line 2, in
from env import resume_env
File "/Users/weizhang/software/ML/Cylinder2DFlowControlWithRL/baseline_flow/env.py", line 10, in
from Env2DCylinder import Env2DCylinder
File "/Users/weizhang/software/ML/Cylinder2DFlowControlWithRL/baseline_flow/../Env2DCylinder.py", line 8, in
from msh_convert import convert
File "/Users/weizhang/software/ML/Cylinder2DFlowControlWithRL/baseline_flow/../msh_convert.py", line 2, in
from dolfin import Mesh, HDF5File, MeshFunction
ImportError: cannot import name HDF5File

Environment (conda list):

# packages in environment at /anaconda2/envs/fenicsproject:
#
# Name                    Version                   Build  Channel
absl-py                   0.7.1                    py27_0    conda-forge
astor                     0.7.1                      py_0    conda-forge
atomicwrites              1.3.0                    pypi_0    pypi
attrs                     19.1.0                   pypi_0    pypi
backports                 1.0                        py_2    conda-forge
backports.weakref         1.0.post1             py27_1000    conda-forge
bleach                    1.5.0                    py27_0    conda-forge
boost                     1.61.0                   py27_2    conda-forge
bzip2                     1.0.6             h1de35cc_1002    conda-forge
c-ares                    1.15.0            h1de35cc_1001    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
certifi                   2019.6.16                py27_0    conda-forge
cmake                     3.14.5               hdd2e4aa_0    conda-forge
configparser              3.7.4                    pypi_0    pypi
contextlib2               0.5.5                    pypi_0    pypi
curl                      7.64.1               h22ea746_0    conda-forge
dijitso                   2016.1.0                 pypi_0    pypi
eigen                     3.3.7             h04f5b5a_1000    conda-forge
enum34                    1.1.6                 py27_1001    conda-forge
expat                     2.2.5             h6de7cb9_1003    conda-forge
fastcache                 1.1.0            py27h01d97ff_0    conda-forge
fenics                    2016.1.0                 py27_2    conda-forge
fiat                      2016.1.0                 pypi_0    pypi
funcsigs                  1.0.2                      py_3    conda-forge
futures                   3.2.0                 py27_1000    conda-forge
gast                      0.2.2                      py_0    conda-forge
gmp                       6.1.2             h0a44026_1000    conda-forge
gmpy2                     2.1.0b1          py27h1744cca_0    conda-forge
grpcio                    1.16.1           py27h044775b_1  
html5lib                  0.9999999                py27_0    conda-forge
icu                       56.1                          4    conda-forge
importlib-metadata        0.18                     pypi_0    pypi
instant                   2016.1.0                 pypi_0    pypi
krb5                      1.16.3            hcfa6398_1001    conda-forge
libblas                   3.8.0                7_openblas    conda-forge
libcblas                  3.8.0                7_openblas    conda-forge
libcurl                   7.64.1               h16faf7d_0    conda-forge
libcxx                    8.0.0                         3    conda-forge
libcxxabi                 8.0.0                         3    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                7_openblas    conda-forge
libprotobuf               3.8.0                hfbae3c0_0    conda-forge
libssh2                   1.8.2                hcdc9a53_2    conda-forge
libuv                     1.30.0               h01d97ff_0    conda-forge
markdown                  2.6.11                     py_0    conda-forge
mock                      3.0.5                    py27_0    conda-forge
more-itertools            5.0.0                    pypi_0    pypi
mpc                       1.1.0             h3aece09_1006    conda-forge
mpfr                      4.0.2                h0a95893_0    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
ncurses                   6.1               h0a44026_1002    conda-forge
numpy                     1.16.4           py27h6b0580a_0    conda-forge
openblas                  0.3.5             h436c29b_1001    conda-forge
openssl                   1.1.1b               h01d97ff_2    conda-forge
packaging                 19.0                     pypi_0    pypi
pathlib2                  2.3.4                    pypi_0    pypi
pcre                      8.41              h0a44026_1003    conda-forge
pillow                    6.0.0                    pypi_0    pypi
pip                       19.1.1                   py27_0    conda-forge
pkg-config                0.29.2            h112b980_1005    conda-forge
pluggy                    0.12.0                   pypi_0    pypi
ply                       3.11                       py_1    conda-forge
printind                  4.0                      pypi_0    pypi
protobuf                  3.8.0            py27h6de7cb9_1    conda-forge
py                        1.8.0                    pypi_0    pypi
pyparsing                 2.4.0                    pypi_0    pypi
pytest                    4.6.3                    pypi_0    pypi
python                    2.7.15            h932b40d_1008    conda-forge
readline                  7.0               hcfe32e1_1001    conda-forge
rhash                     1.3.6             h1de35cc_1001    conda-forge
scandir                   1.10.0                   pypi_0    pypi
scipy                     1.2.2                    pypi_0    pypi
setuptools                41.0.1                   py27_0    conda-forge
six                       1.12.0                py27_1000    conda-forge
sqlite                    3.28.0               h9721f7c_0    conda-forge
swig                      4.0.0                h6de7cb9_0    conda-forge
sympy                     1.4                      py27_0    conda-forge
tensorboard               1.8.0                    py27_1    conda-forge
tensorflow                1.8.0                    py27_1    conda-forge
tensorforce               0.4.2                    pypi_0    pypi
termcolor                 1.1.0                      py_2    conda-forge
tk                        8.6.9             h2573ce8_1002    conda-forge
ufl                       2016.1.0                 pypi_0    pypi
wcwidth                   0.1.7                    pypi_0    pypi
webencodings              0.5.1                      py_1    conda-forge
werkzeug                  0.15.4                     py_0    conda-forge
wheel                     0.33.4                   py27_0    conda-forge
xz                        5.2.4             h1de35cc_1001    conda-forge
zipp                      0.5.1                    pypi_0    pypi
zlib                      1.2.11            h1de35cc_1004    conda-forge

Details about conda and system ( conda info ):

  active environment : fenicsproject
    active env location : /anaconda2/envs/fenicsproject
            shell level : 2
       user config file : /Users/weizhang/.condarc
 populated config files : /Users/weizhang/.condarc
          conda version : 4.7.5
    conda-build version : 3.17.8
         python version : 2.7.16.final.0
       virtual packages : 
       base environment : /anaconda2  (writable)
           channel URLs : 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 : /anaconda2/pkgs
                          /Users/weizhang/.conda/pkgs
       envs directories : /anaconda2/envs
                          /Users/weizhang/.conda/envs
               platform : osx-64
             user-agent : conda/4.7.5 requests/2.21.0 CPython/2.7.16 Darwin/18.2.0 OSX/10.14.2
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Verification fails with python 3.9

• I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

Environment (conda list):

conda create --name my_env -c conda-forge python=3.9 fenics

Details about conda and system ( conda info ):

$ conda info

    active environment : base
    active env location : /users/me/workspace/tools/miniconda
            shell level : 1
       user config file : /users/me/.condarc
 populated config files : 
          conda version : 4.10.3
    conda-build version : 3.21.4
         python version : 3.9.1.final.0
       virtual packages : __linux=3.10.0=0
                          __glibc=2.17=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /users/me/workspace/tools/miniconda  (writable)
      conda av data dir : /users/me/workspace/tools/miniconda/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /users/me/workspace/tools/miniconda/pkgs
                          /users/me/.conda/pkgs
       envs directories : /users/me/workspace/tools/miniconda/envs
                          /users/me/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.3 requests/2.25.1 CPython/3.9.1 Linux/3.10.0-1160.36.2.el7.x86_64 rhel/7.9 glibc/2.17
                UID:GID : 31824:4410
             netrc file : None
           offline mode : False

Trying to install fenics with python 3.9 gives following error.

CondaVerificationError: The package for fenics-ufl located at /users/PAS1064/k09/workspace/tools/miniconda/pkgs/fenics-ufl-2019.1.0-py39hf3d152e_23
appears to be corrupted. The path 'lib/python3.9/site-packages/fenics_ufl-2019.1.0.dist-info/direct_url.json'
specified in the package manifest cannot be found.
CondaVerificationError: The package for fenics-ufl located at /users/PAS1064/k09/workspace/tools/miniconda/pkgs/fenics-ufl-2019.1.0-py39hf3d152e_23
appears to be corrupted. The path 'lib/python3.9/site-packages/fenics_ufl-2019.1.0.dist-info/top_level.txt'
specified in the package manifest cannot be found.
CondaVerificationError: The package for fenics-ufl located at /users/PAS1064/k09/workspace/tools/miniconda/pkgs/fenics-ufl-2019.1.0-py39hf3d152e_23
appears to be corrupted. The path 'lib/python3.9/site-packages/ufl/core/__init__.py'
specified in the package manifest cannot be found.
CondaVerificationError: The package for fenics-ufl located at /users/PAS1064/k09/workspace/tools/miniconda/pkgs/fenics-ufl-2019.1.0-py39hf3d152e_23
appears to be corrupted. The path 'lib/python3.9/site-packages/ufl/corealg/__init__.py'
specified in the package manifest cannot be found.
CondaVerificationError: The package for fenics-ufl located at /users/PAS1064/k09/workspace/tools/miniconda/pkgs/fenics-ufl-2019.1.0-py39hf3d152e_23
appears to be corrupted. The path 'lib/python3.9/site-packages/ufl/formatting/__init__.py'
specified in the package manifest cannot be found.
CondaVerificationError: The package for fenics-ufl located at /users/PAS1064/k09/workspace/tools/miniconda/pkgs/fenics-ufl-2019.1.0-py39hf3d152e_23
appears to be corrupted. The path 'lib/python3.9/site-packages/ufl/measureoperators.py'
specified in the package manifest cannot be found.
CondaVerificationError: The package for fenics-ufl located at /users/PAS1064/k09/workspace/tools/miniconda/pkgs/fenics-ufl-2019.1.0-py39hf3d152e_23
appears to be corrupted. The path 'lib/python3.9/site-packages/ufl/utils/__init__.py'
specified in the package manifest cannot be found.
ClobberError: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/linux-64::suitesparse-5.10.1-h9e50725_1, conda-forge/linux-64::superlu_dist-7.1.1-h25dcc4a_0
  path: 'include/colamd.h'
ClobberError: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/linux-64::superlu-5.2.2-h16cfea0_0, conda-forge/linux-64::superlu_dist-7.1.1-h25dcc4a_0
  path: 'include/superlu_enum_consts.h'
ClobberError: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/linux-64::superlu-5.2.2-h16cfea0_0, conda-forge/linux-64::superlu_dist-7.1.1-h25dcc4a_0
  path: 'include/supermatrix.h'

It works if I constraint python to version 3.7

dependency conflict with pinned anaconda

It seems that when one wants to have environment with pinned anaconda and fenics there is some dependency conflict:

rskolasinski@satriani:~> conda create --name anaconda_fenics_test python=3.5 anaconda=4.3 fenics=2016.2
Fetching package metadata ...........
Solving package specifications: .


UnsatisfiableError: The following specifications were found to be in conflict:
  - anaconda 4.3* -> llvmlite 0.15.0 py27_0
  - anaconda 4.3* -> numba 0.30.1 np111py27_0
  - anaconda 4.3* -> numexpr 2.6.1 np111py27_2
  - anaconda 4.3* -> scikit-learn 0.18.1 np111py27_1
  - fenics 2016.2*
Use "conda info <package>" to see the dependencies for each package.

Adapt version pinning of numpy

fenics is using a different numpy version pinning compared to other projects from the scientific python stack, e.g., scipy/pandas/h5py

https://github.com/conda-forge/scipy-feedstock/pull/100/files
https://github.com/conda-forge/pandas-feedstock/pull/62/files
https://github.com/conda-forge/h5py-feedstock/blob/master/.ci_support/linux_mpiopenmpipython3.7.yaml

The pinned version of numpy should be changed to 1.14.

This will probably fix issues like:

numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject

in code that is built against a newer version of numpy.

libfortran.so.4 error on import fenics

Issue:

I have problem with installing fenics with Anaconda, Ubuntu 16.04. I follow the instructions I found at https://fenicsproject.org/download/, however, when I try to run my python script, I get the following error:

Traceback (most recent call last):
  File "diffusion_K.py", line 1, in <module>
    from fenics import *
  File "/home/ondrej/anaconda3/envs/fenicsproject/lib/python3.6/site-packages/fenics/__init__.py", line 7, in <module>
    from dolfin import *
  File "/home/ondrej/anaconda3/envs/fenicsproject/lib/python3.6/site-packages/dolfin/__init__.py", line 34, in <module>
    from .cpp import __version__
ImportError: libgfortran.so.4: cannot open shared object file: No such file or directory

After trying solution I found online (downgrade libgfortran-ng to version 7.2.0), I get another issue: CXXABI_1.3.9 not included in libstdc++.so.6.

Environment (conda list):

$ conda list
# packages in environment at /home/ondrej/anaconda3/envs/fenicsproject:
#
# Name                    Version                   Build  Channel
blas                      1.1                    openblas    conda-forge
boost                     1.67.0                   py36_4  
bzip2                     1.0.6                h470a237_2    conda-forge
ca-certificates           2018.8.24            ha4d7672_0    conda-forge
certifi                   2018.8.24                py36_1    conda-forge
cloog                     0.18.0                        0  
cmake                     3.12.2               h011004d_0    conda-forge
curl                      7.61.0               h93b3f91_2    conda-forge
eigen                     3.3.5                hfc679d8_1    conda-forge
expat                     2.2.6                he6710b0_0  
fastcache                 1.0.2            py36h470a237_1    conda-forge
fenics                    2018.1.0         py36hba71e3e_1    conda-forge
gcc                       4.8.5                         7  
gmp                       6.1.2                hfc679d8_0    conda-forge
gmpy2                     2.0.8                    py36_1    conda-forge
hdf5                      1.10.2               hc401514_2    conda-forge
hypre                     2.14.0               h7df9f4f_1    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
isl                       0.12.2                        0  
krb5                      1.14.6                        0    conda-forge
libboost                  1.67.0               h46d08c1_4  
libffi                    3.2.1                hfc679d8_5    conda-forge
libgcc-ng                 8.2.0                hdf63c60_1  
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            8.2.0                hdf63c60_1  
libssh2                   1.8.0                h5b517e9_2    conda-forge
libstdcxx-ng              8.2.0                hdf63c60_1  
libuv                     1.23.0               h7b6447c_0  
metis                     5.1.0                h470a237_3    conda-forge
mpc                       1.1.0                         4    conda-forge
mpfr                      3.1.5                         0    conda-forge
mpi                       1.0                       mpich    conda-forge
mpi4py                    3.0.0              py36_mpich_3    conda-forge
mpich                     3.2.1                h26a2512_4    conda-forge
mpmath                    1.0.0                      py_0    conda-forge
mumps-mpi                 5.1.2           blas_openblasha5050ec_0  [blas_openblas]  conda-forge
ncurses                   6.1                  hfc679d8_1    conda-forge
numpy                     1.14.5          py36_blas_openblashd3ea46f_202  [blas_openblas]  conda-forge
openblas                  0.2.20                        8    conda-forge
openssl                   1.0.2p               h470a237_0    conda-forge
parmetis                  4.0.3                hf0665dc_2    conda-forge
petsc                     3.9.3           blas_openblash330393b_1  [blas_openblas]  conda-forge
petsc4py                  3.9.1            py36h18b3941_1    conda-forge
pip                       18.0                     py36_1    conda-forge
pkg-config                0.29.2               h470a237_3    conda-forge
pkgconfig                 1.4.0                    py36_0  
ptscotch                  6.0.5                ha5050ec_0    conda-forge
py-boost                  1.67.0           py36h04863e7_4  
pybind11                  2.2.4            py36h2d50403_1    conda-forge
python                    3.6.6                h5001a0f_0    conda-forge
readline                  7.0                  haf1bffa_1    conda-forge
rhash                     1.3.6                hb7f436b_0  
scalapack                 2.0.2                h186ce0b_3    conda-forge
scotch                    6.0.5                h9c0d707_1    conda-forge
setuptools                40.2.0                   py36_0    conda-forge
six                       1.11.0                   py36_1    conda-forge
slepc                     3.9.2           blas_openblashe63b0ae_0  [blas_openblas]  conda-forge
slepc4py                  3.9.0            py36h7eb728f_1    conda-forge
sqlite                    3.24.0               h2f33b56_1    conda-forge
suitesparse               4.5.6           blas_openblash55dcaef_201  [blas_openblas]  conda-forge
sympy                     1.1.1                    py36_0    conda-forge
tbb                       2018_20171205                 0    conda-forge
tk                        8.6.8                         0    conda-forge
wheel                     0.31.1                   py36_1    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

Details about conda and system ( conda info ):

$ conda info

     active environment : fenicsproject
    active env location : /home/ondrej/anaconda3/envs/fenicsproject
            shell level : 1
       user config file : /home/ondrej/.condarc
 populated config files : /home/ondrej/.condarc
          conda version : 4.5.11
    conda-build version : 3.10.5
         python version : 3.6.5.final.0
       base environment : /home/ondrej/anaconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /home/ondrej/anaconda3/pkgs
                          /home/ondrej/.conda/pkgs
       envs directories : /home/ondrej/anaconda3/envs
                          /home/ondrej/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.11 requests/2.18.4 CPython/3.6.5 Linux/4.4.0-135-generic ubuntu/16.04 glibc/2.23
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Add packages for python 3.8

Issue:

It is not yet possible to install fenics in a python3.8 conda env.

Environment (conda list):

$ conda list

Details about conda and system ( conda info ):

$ conda info

after installing `fenics=2017.2`, `mumps-mpi` breaks other packages that depend on `mumps`

Installing fenics=2017.2, also installs mumps-mpi,
which makes my installation of kwant=dev stop working.

Another way is to install fenics=2007.2, and build kwant
from source. In this case, inside a python shell, if you import kwant
it warns about not having mumps installed. But if you
import fenics; import kwant then there is no issue.

Here a snippet to reproduce the bug.

Installing kwant from kwant channel and fenics from conda-forge

$ conda create -n test_fenics python=3.6 fenics=2017.2 kwant=dev
... after installing
$ conda activate test_fenics
$ python -c 'import kwant; print(hasattr(kwant.linalg, "mumps"))'
> True
$ python -c 'import fenics; import kwant'
> ** ERROR RETURN ** FROM ZMUMPS INFO(1)=   -3
> ** INFO(2)=        -1
(n times)

Building kwant from source, and installing fenics from conda-forge (continue with previous env)

$ conda uninstall kwant
$ conda install cython && pip install git+ssh://[email protected]:443/kwant/kwant.git
$ python -c 'import kwant; print(hasattr(kwant.linalg, "mumps"))'
> RuntimeWarning: MUMPS is not available, SciPy built-in solver will be used as a fallback.
   Performance can be very poor in this case.
> False
$ python -c 'import fenics; import kwant'
>

PackagesNotFoundError: fenics

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

I can't install fenics.

Running:

conda install -c conda-forge fenics

Produces:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.  

PackagesNotFoundError: The following packages are not available from current channels:

  - fenics

Current channels:

  - https://conda.anaconda.org/conda-forge/win-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Installed packages

asteval                   0.9.27                   pypi_0    pypi
asttokens                 2.0.5              pyhd8ed1ab_0    conda-forge
atomicwrites              1.4.0                    pypi_0    pypi
attrs                     21.4.0                   pypi_0    pypi
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
brotli                    1.0.9                    pypi_0    pypi
brotlipy                  0.7.0           py39h2bbff1b_1003
bzip2                     1.0.8                h8ffe710_4    conda-forge
ca-certificates           2021.10.8            h5b45459_0    conda-forge
cadquery                  master                    py3.9    cadquery
certifi                   2021.10.8        py39hcbf5309_2    conda-forge
cffi                      1.15.0           py39h2bbff1b_0
cftime                    1.6.0                    pypi_0    pypi
charset-normalizer        2.0.4              pyhd3eb1b0_0
click                     8.1.3                    pypi_0    pypi
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
commonmark                0.9.1                    pypi_0    pypi
conda                     4.12.0           py39hcbf5309_0    conda-forge
conda-content-trust       0.1.1              pyhd3eb1b0_0
conda-package-handling    1.7.3            py39h8cc25b3_1
console_shortcut          0.1.1                         4
cryptography              36.0.0           py39h21b164f_0
curl                      7.82.0               h789b8ee_0    conda-forge
cycler                    0.11.0                   pypi_0    pypi
dash                      2.4.1                    pypi_0    pypi
dash-bootstrap-components 1.1.0                    pypi_0    pypi
dash-core-components      2.0.0                    pypi_0    pypi
dash-html-components      2.0.0                    pypi_0    pypi
dash-table                5.0.0                    pypi_0    pypi
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
double-conversion         3.1.7                h0e60522_0    conda-forge
eigen                     3.4.0                h2d74725_0    conda-forge
executing                 0.8.3              pyhd8ed1ab_0    conda-forge
expat                     2.4.8                h39d44d4_0    conda-forge
ezdxf                     0.17.2           py39h2e07f2f_1    conda-forge
ffmpeg                    4.3.1                ha925a31_0    conda-forge
flask                     2.1.2                    pypi_0    pypi
flask-compress            1.12                     pypi_0    pypi
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.0               hce3cb01_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.33.3                   pypi_0    pypi
freeimage                 3.18.0               h6676e37_8    conda-forge
freetype                  2.10.4               h546665d_1    conda-forge
future                    0.18.2                   pypi_0    pypi
gl2ps                     1.4.2                h0597ee9_0    conda-forge
glew                      2.1.0                h39d44d4_2    conda-forge
gmsh                      4.10.5                   pypi_0    pypi
gunicorn                  20.1.0                   pypi_0    pypi
h-transport-materials     0.2                      pypi_0    pypi
h5py                      3.7.0                    pypi_0    pypi
hdf4                      4.2.15               h0e5069d_3    conda-forge
hdf5                      1.10.6          nompi_h5268f04_1114    conda-forge
icu                       69.1                 h0e60522_0    conda-forge
idna                      3.3                pyhd3eb1b0_0
imath                     3.1.5                h12d4b20_0    conda-forge
importlib-metadata        4.11.4                   pypi_0    pypi
iniconfig                 1.1.1                    pypi_0    pypi
intel-openmp              2022.0.0          h57928b3_3663    conda-forge
ipython                   8.2.0            py39hcbf5309_0    conda-forge
itsdangerous              2.1.2                    pypi_0    pypi
jbig                      2.1               h8d14728_2003    conda-forge
jedi                      0.18.1           py39hcbf5309_1    conda-forge
jinja2                    3.1.1                    pypi_0    pypi
jpeg                      9e                   h8ffe710_1    conda-forge
jsoncpp                   1.9.4                h2d74725_3    conda-forge
jxrlib                    1.1                  h8ffe710_2    conda-forge
kiwisolver                1.4.2                    pypi_0    pypi
krb5                      1.19.3               h1176d77_0    conda-forge
lcms2                     2.12                 h2a16943_0    conda-forge
lerc                      3.0                  h0e60522_0    conda-forge
libblas                   3.9.0                     8_mkl    conda-forge
libcblas                  3.9.0                     8_mkl    conda-forge
libclang                  13.0.1          default_h81446c8_0    conda-forge
libcurl                   7.82.0               h789b8ee_0    conda-forge
libdeflate                1.10                 h8ffe710_0    conda-forge
libiconv                  1.16                 he774522_0    conda-forge
liblapack                 3.9.0                     8_mkl    conda-forge
libnetcdf                 4.8.1           nompi_hf689e7d_100    conda-forge
libogg                    1.3.4                h8ffe710_1    conda-forge
libpng                    1.6.37               h1d00b33_2    conda-forge
libraw                    0.20.2               hee1bdec_1    conda-forge
libssh2                   1.10.0               h680486a_2    conda-forge
libtheora                 1.1.1             h8d14728_1005    conda-forge
libtiff                   4.3.0                hc4061b1_3    conda-forge
libwebp-base              1.2.2                h8ffe710_1    conda-forge
libxml2                   2.9.13               hf5bbc77_0    conda-forge
libzip                    1.8.0                hfed4ece_1    conda-forge
libzlib                   1.2.11            h8ffe710_1014    conda-forge
loguru                    0.6.0            py39hcbf5309_1    conda-forge
lxml                      4.9.0                    pypi_0    pypi
lz4-c                     1.9.3                h8ffe710_1    conda-forge
markupsafe                2.1.1                    pypi_0    pypi
matplotlib                3.5.2                    pypi_0    pypi
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
matplotlib-label-lines    0.5.1                    pypi_0    pypi
matplotx                  0.3.7                    pypi_0    pypi
menuinst                  1.4.18           py39h59b6b97_0
meshio                    5.3.4                    pypi_0    pypi
mkl                       2020.4             hb70f87d_311    conda-forge
more-itertools            8.13.0                   pypi_0    pypi
multimethod               1.6                pyhd8ed1ab_0    conda-forge
netcdf4                   1.5.8                    pypi_0    pypi
neutronics-material-maker 1.1.1                    pypi_0    pypi
nlopt                     2.7.1            py39h6714f1b_0    conda-forge
nptyping                  2.0.0              pyhd8ed1ab_0    conda-forge
numpy                     1.22.3           py39h6331f09_2    conda-forge
occt                      7.5.3                h60997fb_0    conda-forge
ocp                       7.5.3.0          py39haf71b9b_2    conda-forge
openexr                   3.1.5                hab3b255_0    conda-forge
openjpeg                  2.4.0                hb211442_1    conda-forge
openssl                   1.1.1n               h8ffe710_0    conda-forge
packaging                 21.3                     pypi_0    pypi
pandas                    1.4.3                    pypi_0    pypi
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.1.0                    pypi_0    pypi
pip                       21.2.4           py39haa95532_0
plotly                    5.8.0                    pypi_0    pypi
pluggy                    1.0.0                    pypi_0    pypi
powershell_shortcut       0.0.1                         3
proj                      7.2.0                h1cfcee9_2    conda-forge
prompt-toolkit            3.0.29             pyha770c72_0    conda-forge
pugixml                   1.11.4               h0e60522_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py                        1.11.0                   pypi_0    pypi
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.3            py39h2bbff1b_0
pycparser                 2.21               pyhd3eb1b0_0
pyenergydiagrams          1.0.1                    pypi_0    pypi
pygments                  2.11.2             pyhd8ed1ab_0    conda-forge
pyopenssl                 21.0.0             pyhd3eb1b0_1
pyparsing                 3.0.8              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py39haa95532_0
pytest                    7.1.2                    pypi_0    pypi
python                    3.9.7                h6244533_1
python-dateutil           2.8.2                    pypi_0    pypi
python_abi                3.9                      2_cp39    conda-forge
pytz                      2022.1                   pypi_0    pypi
pywin32                   302              py39h827c3e9_1
qt                        5.12.9               h556501e_6    conda-forge
rapidjson                 1.1.0             ha925a31_1002    conda-forge
requests                  2.27.1             pyhd3eb1b0_0
rich                      12.4.4                   pypi_0    pypi
ruamel_yaml               0.15.100         py39h2bbff1b_0
scipy                     1.8.0                    pypi_0    pypi
setuptools                58.0.4           py39haa95532_0
six                       1.16.0             pyhd3eb1b0_0
sqlite                    3.37.0               h2bbff1b_0
stack_data                0.2.0              pyhd8ed1ab_0    conda-forge
tbb                       2020.2               h2d74725_4    conda-forge
tbb-devel                 2020.2               h2d74725_4    conda-forge
tenacity                  8.0.1                    pypi_0    pypi
tomli                     2.0.1                    pypi_0    pypi
tqdm                      4.62.3             pyhd3eb1b0_1
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
typing_extensions         4.2.0              pyha770c72_1    conda-forge
typish                    1.9.3              pyhd8ed1ab_0    conda-forge
tzdata                    2021e                hda174b7_0
uncertainties             3.1.7                    pypi_0    pypi
urllib3                   1.26.7             pyhd3eb1b0_0
utfcpp                    3.2.1                h57928b3_0    conda-forge
vc                        14.2                 h21ff451_1
vs2015_runtime            14.27.29016          h5e58377_2
vtk                       9.0.1           qt_py39hbb6573b_210    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
werkzeug                  2.1.2                    pypi_0    pypi
wheel                     0.37.1             pyhd3eb1b0_0
win32_setctime            1.1.0              pyhd8ed1ab_0    conda-forge
win_inet_pton             1.1.0            py39haa95532_0
wincertstore              0.2              py39haa95532_2
xz                        5.2.5                h62dcd97_1    conda-forge
yaml                      0.2.5                he774522_0
zipp                      3.8.0                    pypi_0    pypi
zlib                      1.2.11            h8ffe710_1014    conda-forge
zstd                      1.5.2                h6255e5f_0    conda-forge

Environment info

active environment : base
    active env location : C:\Users\rdelaporte\Miniconda3
            shell level : 1
       user config file : C:\Users\rdelaporte\.condarc
 populated config files :
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.7.final.0
       virtual packages : __cuda=11.6=0
                          __win=0=0
                          __archspec=1=x86_64
       base environment : C:\Users\rdelaporte\Miniconda3  (writable)
      conda av data dir : C:\Users\rdelaporte\Miniconda3\etc\conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
          package cache : C:\Users\rdelaporte\Miniconda3\pkgs
                          C:\Users\rdelaporte\.conda\pkgs
                          C:\Users\rdelaporte\AppData\Local\conda\conda\pkgs
       envs directories : C:\Users\rdelaporte\Miniconda3\envs
                          C:\Users\rdelaporte\.conda\envs
                          C:\Users\rdelaporte\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.7 Windows/10 Windows/10.0.19043
          administrator : False
             netrc file : None
           offline mode : False

is gcc, cmake really needed at runtime?

ImportError: libhdf5.so.10: cannot open shared object file: No such file or directory

After adding HDF5 the other day everything seemed to be working fine, however, now I get this error when importing dolfin:

$ python -c "import dolfin"
Traceback (most recent call last):
  File "/home/johannr/miniconda2/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/cpp/common.py", line 18, in swig_import_helper
    return importlib.import_module(mname)
  File "/home/johannr/miniconda2/envs/fenicsproject-py36/lib/python3.6/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 978, in _gcd_import
  File "<frozen importlib._bootstrap>", line 961, in _find_and_load
  File "<frozen importlib._bootstrap>", line 950, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 648, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 560, in module_from_spec
  File "<frozen importlib._bootstrap_external>", line 922, in create_module
  File "<frozen importlib._bootstrap>", line 205, in _call_with_frames_removed
ImportError: libhdf5.so.10: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/johannr/miniconda2/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/__init__.py", line 17, in <module>
    from . import cpp
  File "/home/johannr/miniconda2/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/cpp/__init__.py", line 43, in <module>
    exec("from . import %s" % module_name)
  File "<string>", line 1, in <module>
  File "/home/johannr/miniconda2/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/cpp/common.py", line 21, in <module>
    _common = swig_import_helper()
  File "/home/johannr/miniconda2/envs/fenicsproject-py36/lib/python3.6/site-packages/dolfin/cpp/common.py", line 20, in swig_import_helper
    return importlib.import_module('_common')
  File "/home/johannr/miniconda2/envs/fenicsproject-py36/lib/python3.6/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ModuleNotFoundError: No module named '_common'

I see that a new version of HDF5 was uploaded yesterday (in PR #73) and that could be the reason for this error.

importing fenics fails because a shared libary is not made

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$ 
</code>

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

include mshr?

Should we be including mshr in the fenics package?

unable to install in base-notebook for Jupyterhub

In trying to setup a Jupyterhub using the provided base-notebook I get the following error:

Linking packages ...
/opt/conda/bin/.gcc-post-link.sh: line 10: lsb_release: command not found###############################################################################                                                  |  72%
/opt/conda/bin/.gcc-post-link.sh: line 49: ld: command not found
Couldn't locate crtXXX.o in default library search paths. You may not have it  at all. It is usually packaged in libc6-dev/glibc-devel packages. We will try  to locate crtXXX.o with system installed gcc...
There is no /usr/bin/gcc
*** Can't install the gcc package unless your system has crtXXX.o. ***


LinkError: Link error: Error: post-link failed for: gcc-4.8.5-7

reproduce with:

docker run -it --rm --user root jupyter/base-notebook bash
conda install --yes fenics

or

env.yml:

name: python3
channels:
  - conda-forge
dependencies:
  - fenics

Dockerfile:

FROM jupyter/base-notebook
USER root
COPY env.yml env.yml
RUN conda env update -n root -f env.yml