Hello everybody,
I am trying to install fenics on my mac (m1 processor) I have come to activate fenicsproject but when I try to run the first simulation (demo_poisson.py) I get the following error message:
Traceback (most recent call last):
File "demo_poisson.py", line 79, in <module>
from dolfin import *
ModuleNotFoundError: No module named 'dolfin'
Where is the problem? What do you suggest me to do?
Please add a more detailed description of how you installed fenics on your computer, adding the list of commands you ran to install fenics.
If you found the instructions on a web page, please add the link for reference (for instance https://fenicsproject.org/download/archive/), and which of the paths here you followed.
Please also report the output of pip3 list
I tried to install fenics with the FEniCS on Anaconda procedure (described in the link indicated):
conda create -n fenicsproject -c conda-forge fenics
source activate fenicsproject
Next I ran the command:
conda activate fenicsproject and lastly, after downloading "demo_poisson.py from https://fenicsproject.org/olddocs/dolfin/latest/python/installation.html#quick-start I tried to run it simply with command: python demo_poisson.py
The output of pip3 list is:
Package Version
--------------- -------------
fenics-dijitso 2019.2.0.dev0
fenics-ffc 2019.2.0.dev0
fenics-fiat 2019.2.0.dev0
fenics-ufl 2021.2.0.dev0
mpmath 1.2.1
numpy 1.22.2
pandas 1.4.1
pip 21.3.1
pycairo 1.20.1
pydicom 2.2.2
PyGObject 3.42.0
python-dateutil 2.8.2
pytz 2021.3
scipy 1.8.0
setuptools 60.5.0
six 1.16.0
sympy 1.9
wheel 0.37.1
```Im suprised by the outputted version of the fenics dependencies, as they are not in the conda-forge https://anaconda.org/conda-forge/fenics/labels as far as Im aware.
Could you post the output of running:
conda create -n fenicsproject -c conda-forge fenics
WARNING: A conda environment already exists at '/Applications/anaconda3/envs/fenicsproject'
Remove existing environment (y/[n])? y
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Applications/anaconda3/envs/fenicsproject
added / updated specs:
- fenics
The following NEW packages will be INSTALLED:
boost-cpp conda-forge/osx-64::boost-cpp-1.74.0-hdbf7018_7
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
c-ares conda-forge/osx-64::c-ares-1.18.1-h0d85af4_0
ca-certificates conda-forge/osx-64::ca-certificates-2021.10.8-h033912b_0
cmake conda-forge/osx-64::cmake-3.22.2-h4d639be_0
eigen conda-forge/osx-64::eigen-3.4.0-h940c156_0
expat conda-forge/osx-64::expat-2.4.6-h96cf925_0
fenics conda-forge/osx-64::fenics-2019.1.0-py39h6e9494a_26
fenics-dijitso conda-forge/osx-64::fenics-dijitso-2019.1.0-py39h6e9494a_26
fenics-dolfin conda-forge/osx-64::fenics-dolfin-2019.1.0-py39h1caa1a8_26
fenics-ffc conda-forge/osx-64::fenics-ffc-2019.1.0-py39h6e9494a_26
fenics-fiat conda-forge/osx-64::fenics-fiat-2019.1.0-py39h6e9494a_26
fenics-libdolfin conda-forge/osx-64::fenics-libdolfin-2019.1.0-h0741ba5_26
fenics-ufl conda-forge/osx-64::fenics-ufl-2019.1.0-py39h6e9494a_26
fftw conda-forge/osx-64::fftw-3.3.10-mpi_mpich_he67630e_2
gmp conda-forge/osx-64::gmp-6.2.1-h2e338ed_0
gmpy2 conda-forge/osx-64::gmpy2-2.1.2-py39hab8a6df_0
hdf5 conda-forge/osx-64::hdf5-1.10.6-mpi_mpich_h8c5dddf_1013
hypre conda-forge/osx-64::hypre-2.23.0-mpi_mpich_hfb0abaf_0
icu conda-forge/osx-64::icu-69.1-he49afe7_0
krb5 conda-forge/osx-64::krb5-1.19.2-hcfbf3a7_3
libblas conda-forge/osx-64::libblas-3.9.0-13_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-13_osx64_openblas
libcurl conda-forge/osx-64::libcurl-7.81.0-hf45b732_0
libcxx conda-forge/osx-64::libcxx-12.0.1-habf9029_1
libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2
libev conda-forge/osx-64::libev-4.33-haf1e3a3_1
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libgfortran conda-forge/osx-64::libgfortran-5.0.0-9_3_0_h6c81a4c_23
libgfortran5 conda-forge/osx-64::libgfortran5-9.3.0-h6c81a4c_23
libiconv conda-forge/osx-64::libiconv-1.16-haf1e3a3_0
liblapack conda-forge/osx-64::liblapack-3.9.0-13_osx64_openblas
libnghttp2 conda-forge/osx-64::libnghttp2-1.47.0-h942079c_0
libopenblas conda-forge/osx-64::libopenblas-0.3.18-openmp_h3351f45_0
libssh2 conda-forge/osx-64::libssh2-1.10.0-h52ee1ee_2
libuv conda-forge/osx-64::libuv-1.43.0-h0d85af4_0
libzlib conda-forge/osx-64::libzlib-1.2.11-h9173be1_1013
llvm-openmp conda-forge/osx-64::llvm-openmp-13.0.1-hda6cdc1_0
lz4-c conda-forge/osx-64::lz4-c-1.9.3-he49afe7_1
metis conda-forge/osx-64::metis-5.1.0-h2e338ed_1006
mpc conda-forge/osx-64::mpc-1.2.1-hbb51d92_0
mpfr conda-forge/osx-64::mpfr-4.1.0-h0f52abe_1
mpi conda-forge/osx-64::mpi-1.0-mpich
mpi4py conda-forge/osx-64::mpi4py-3.1.3-py39ha81d895_0
mpich conda-forge/osx-64::mpich-3.4.3-hd33e60e_100
mpmath conda-forge/noarch::mpmath-1.2.1-pyhd8ed1ab_0
mumps-include conda-forge/osx-64::mumps-include-5.2.1-h694c41f_10
mumps-mpi conda-forge/osx-64::mumps-mpi-5.2.1-hae6d205_10
ncurses conda-forge/osx-64::ncurses-6.3-he49afe7_0
numpy conda-forge/osx-64::numpy-1.22.2-py39h9d9ce41_0
openssl conda-forge/osx-64::openssl-1.1.1l-h0d85af4_0
parmetis conda-forge/osx-64::parmetis-4.0.3-hb7fa8f8_1005
petsc conda-forge/osx-64::petsc-3.16.1-real_hecba10c_101
petsc4py conda-forge/osx-64::petsc4py-3.16.1-real_hba9dac2_100
pip conda-forge/noarch::pip-22.0.3-pyhd8ed1ab_0
pkg-config conda-forge/osx-64::pkg-config-0.29.2-h31203cd_1008
pkgconfig conda-forge/osx-64::pkgconfig-1.5.5-py39h6e9494a_1
ptscotch conda-forge/osx-64::ptscotch-6.0.9-h5077668_1
pybind11 pkgs/main/osx-64::pybind11-2.8.1-py39haf03e11_0
python conda-forge/osx-64::python-3.9.10-h1dd9edd_2_cpython
python_abi conda-forge/osx-64::python_abi-3.9-2_cp39
readline conda-forge/osx-64::readline-8.1-h05e3726_0
rhash conda-forge/osx-64::rhash-1.4.1-h35c211d_0
scalapack conda-forge/osx-64::scalapack-2.1.0-hb62163f_0
scotch conda-forge/osx-64::scotch-6.0.9-h9f43b6f_1
setuptools conda-forge/osx-64::setuptools-60.9.3-py39h6e9494a_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
slepc conda-forge/osx-64::slepc-3.16.1-real_ha131d38_101
slepc4py conda-forge/osx-64::slepc4py-3.16.1-real_h776a5bf_100
sqlite conda-forge/osx-64::sqlite-3.37.0-h23a322b_0
suitesparse conda-forge/osx-64::suitesparse-5.10.1-h7aff33d_1
superlu conda-forge/osx-64::superlu-5.2.2-h621599f_0
superlu_dist conda-forge/osx-64::superlu_dist-7.2.0-h4bb6bf2_0
sympy conda-forge/osx-64::sympy-1.9-py39h6e9494a_1
tbb conda-forge/osx-64::tbb-2021.5.0-h940c156_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
tzdata conda-forge/noarch::tzdata-2021e-he74cb21_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
yaml conda-forge/osx-64::yaml-0.2.5-h0d85af4_2
zlib conda-forge/osx-64::zlib-1.2.11-h9173be1_1013
zstd conda-forge/osx-64::zstd-1.5.2-h582d3a0_0
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate fenicsproject
#
# To deactivate an active environment, use
#
# $ conda deactivate
Here it installs the 2019.1.0 version of dolfin, while your pip3 list points to the 2019.2.0.dev0 version of dolfin.
Could you now post the output of
conda activate fenicsproject
followed by
pip3 list
and
which pip3
(base) Mac:~ lorenzomarta$ conda activate fenicsproject
(fenicsproject) Mac:~ lorenzomarta$ pip3 list
Package Version
--------------- -------------
fenics-dijitso 2019.2.0.dev0
fenics-ffc 2019.2.0.dev0
fenics-fiat 2019.2.0.dev0
fenics-ufl 2021.2.0.dev0
mpmath 1.2.1
numpy 1.22.2
pandas 1.4.1
pip 21.3.1
pycairo 1.20.1
pydicom 2.2.2
PyGObject 3.42.0
python-dateutil 2.8.2
pytz 2021.3
scipy 1.8.0
setuptools 60.5.0
six 1.16.0
sympy 1.9
wheel 0.37.1
WARNING: You are using pip version 21.3.1; however, version 22.0.3 is available.
You should consider upgrading via the '/opt/homebrew/opt/python@3.9/bin/python3.9 -m pip install --upgrade pip' command.
(fenicsproject) Mac:~ lorenzomarta$ which pip3
/opt/homebrew/bin/pip3
i just updated pip to version 22.0.3. The output is the same except for package pip version 22.0.3
If you call which pip3 outside the conda environment, what path do you then get?
To me it looks like the PYTHONPATH is not updated correctly when activating the conda environment.
As I do not have a mac, and rarely uses conda, I can’t give much further assistance. Maybe @dparsons or @jackhale knows more about this than I do.
I have found a solution. I’m not sure what the basic computer theory behind it is but it seems to work.
It is necessary, before activating fenicsproject, to deactivate (base) which “dominates” the other environment.
So just run the following commands:
conda deactivates
conda activate fenicsproject
Check the $PATH env variable. Prior to activating the environment, you should have conda in your path:
(base) root@e0730920c745:/fenics# which python3
/root/anaconda3/bin/python3
(base) root@e0730920c745:/fenics# echo $PYTHONPATH
/usr/local/dolfinx-real/lib/python3.8/dist-packages:/usr/local/lib:
while after activating the environment, the path should point to the envirionment you have created, as shown below:
(base) root@e0730920c745:/fenics# conda activate fenicsproject
(fenicsproject) root@e0730920c745:/fenics# echo $PYTHONPATH
/usr/local/dolfinx-real/lib/python3.8/dist-packages:/usr/local/lib:
(fenicsproject) root@e0730920c745:/fenics# echo $PATH
/root/anaconda3/envs/fenicsproject/bin:/root/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
(fenicsproject) root@e0730920c745:/fenics# which python3
/root/anaconda3/envs/fenicsproject/bin/python3
Similarly the python3 should be the one in /root/anaconda3/envs/fenicsproject.