clm
January 27, 2023, 1:41am
1
Hi all,
I’m trying to get fenics to work on my m1 mac using conda.this link from the fenics homepage, I ran:
conda create -n fenicsx-env
conda activate fenicsx-env
conda install -c conda-forge fenics-dolfinx mpich pyvista
Then, I activate using conda activate fenicsx-envsource activate to no avail)python3 demo_poisson.py always leads to the following error:
File "/Users/myname/Downloads/demo_poisson.py", line 37, in <module>
from dolfin import *
ModuleNotFoundError: No module named 'dolfin'
I’ve wondered if the resolution here could be related to my issue. Although the environment has loaded, os.environ['PATH'] returns:
/Users/myname/opt/anaconda3/envs/fenicsx-env/bin:/Users/myname/opt/anaconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin
Which isn’t the same as what is is in that post,
I’ve looked through the other posts on here with similar issues but the things that have worked for them don’t appear to be working for me. I feel a bit silly as I’ve been using python for many years and am yet to have such an issue installing something… Any insight would be lovely.
Thanks!
Hi,
you are using the command from the legacy fenics. To import dolfinx do
from dolfinx import *
which I don’t really recommend. You can refer to this excellent tutorial on how to use dolfinx from this link
https://jsdokken.com/dolfinx-tutorial/
1 Like
You have installed FEniCSx on conda. The FEniCSx tutorial is available here- The FEniCSx tutorial — FEniCSx tutorial . There are more demos available here- Demos — DOLFINx 0.6.0.0 documentation .
from dolfin import *
is actually from Legacy FEniCS. You can also install Legacy FEniCS on conda from here- https://fenicsproject.org/download/archive/ . Legacy FEniCS demos are available here- https://fenicsproject.org/olddocs/dolfin/1.6.0/python/demo/index.html
Hi,
I followed the same installation procedure (conda install on M1 mac) and it went smoothly.
File "/Users/fwaharte/Downloads/demo_poisson.py", line 72, in <module>
from dolfinx import fem, io, mesh, plot
ModuleNotFoundError: No module named 'dolfinx'
I don’t know how to make it work.
Any suggestion would be greatly appreciated
dokken
February 23, 2023, 12:33pm
5
Could you list the packages in the environment you created? Similar to No module named 'dolfin' on Jupyter notebook - #14 by Elizabeth_Hawkins
Sure!
Here is the output of the commande
conda list -n fenicsx-env
# packages in environment at /Users/fwaharte/mambaforge3/envs/fenicsx-env:
#
# Name Version Build Channel
appdirs 1.4.4 pyhd3eb1b0_0
blas 2.116 openblas conda-forge
blas-devel 3.9.0 16_osxarm64_openblas conda-forge
blosc 1.21.3 h1d6ff8b_0 conda-forge
boost-cpp 1.74.0 h32e41df_4 conda-forge
brotlipy 0.7.0 py310h1a28f6b_1002
bzip2 1.0.8 h620ffc9_4
c-ares 1.18.1 h1a28f6b_0
ca-certificates 2022.12.7 h4653dfc_0 conda-forge
certifi 2022.12.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py310h80987f9_3
charset-normalizer 2.0.4 pyhd3eb1b0_0
cryptography 38.0.4 py310h834c97f_0
curl 7.87.0 h80987f9_0
double-conversion 3.1.5 hc377ac9_1
eigen 3.3.7 h525c30c_1
expat 2.4.9 hc377ac9_0
fenics-basix 0.5.1 py310h2887b22_1 conda-forge
fenics-dolfinx 0.5.2 py310hd290994_100 conda-forge
fenics-ffcx 0.5.0 pyhb871ab6_1 conda-forge
fenics-libbasix 0.5.1 hf081368_1 conda-forge
fenics-libdolfinx 0.5.2 h4bbba74_100 conda-forge
fenics-ufcx 0.5.0 hb871ab6_1 conda-forge
fenics-ufl 2022.2.0 pyhd8ed1ab_0 conda-forge
ffmpeg 4.2.2 h04105a8_0
fftw 3.3.10 mpi_mpich_h0cb5807_6 conda-forge
flit-core 3.6.0 pyhd3eb1b0_0
freetype 2.12.1 h1192e45_0
gettext 0.21.0 h826f4ad_0
giflib 5.2.1 h80987f9_3
gl2ps 1.4.2 h1192e45_1
glew 2.1.0 hc377ac9_3
gmp 6.2.1 hc377ac9_3
gnutls 3.6.15 h887c41c_0
hdf4 4.2.13 h5e329fb_3
hdf5 1.12.1 mpi_mpich_h102acf4_4 conda-forge
hypre 2.25.0 mpi_mpich_h060cf3c_0 conda-forge
icu 68.1 hc377ac9_0
idna 3.4 py310hca03da5_0
imageio 2.19.3 py310hca03da5_0
jpeg 9e h1a28f6b_0
jsoncpp 1.9.4 h525c30c_2
krb5 1.19.4 h8380606_0
lame 3.100 h1a28f6b_0
lcms2 2.12 hba8e193_0
lerc 3.0 hc377ac9_0
libadios2 2.8.3 mpi_mpich_h903a2e2_1 conda-forge
libblas 3.9.0 16_osxarm64_openblas conda-forge
libcblas 3.9.0 16_osxarm64_openblas conda-forge
libcurl 7.87.0 h0f1d93c_0
libcxx 14.0.6 h848a8c0_0
libdeflate 1.8 h1a28f6b_5
libedit 3.1.20221030 h80987f9_0
libev 4.33 h1a28f6b_1
libffi 3.4.2 hca03da5_6
libgfortran 5.0.0 11_3_0_hca03da5_28
libgfortran5 11.3.0 h009349e_28
libiconv 1.16 h1a28f6b_2
libidn2 2.3.1 h1a28f6b_0
liblapack 3.9.0 16_osxarm64_openblas conda-forge
liblapacke 3.9.0 16_osxarm64_openblas conda-forge
libnetcdf 4.8.1 h1b8e529_2
libnghttp2 1.46.0 h95c9599_0
libogg 1.3.5 h1a28f6b_1
libopenblas 0.3.21 openmp_hc731615_3 conda-forge
libopus 1.3 h1a28f6b_1
libpng 1.6.37 hb8d0fd4_0
libsodium 1.0.18 h27ca646_1 conda-forge
libsqlite 3.40.0 h76d750c_0 conda-forge
libssh2 1.10.0 hf27765b_0
libtasn1 4.16.0 h1a28f6b_0
libtheora 1.1.1 h1a28f6b_3
libtiff 4.5.0 h313beb8_1
libunistring 0.9.10 h1a28f6b_0
libvorbis 1.3.7 h1a28f6b_0
libvpx 1.10.0 hc377ac9_0
libwebp 1.2.4 ha3663a8_1
libwebp-base 1.2.4 h80987f9_1
libxml2 2.9.14 h8c5e841_0
libzip 1.8.0 h0c481fb_0
libzlib 1.2.13 h03a7124_4 conda-forge
llvm-openmp 14.0.6 hc6e5704_0
loguru 0.5.3 py310hca03da5_4
lz4-c 1.9.4 h313beb8_0
metis 5.1.0 h9f76cd9_1006 conda-forge
mpfr 4.1.0 h6d7a090_1 conda-forge
mpi 1.0 mpich
mpi4py 3.1.4 py310hb6d4c64_0 conda-forge
mpich 4.0.3 hd4b5bf3_100 conda-forge
mumps-include 5.2.1 hce30654_11 conda-forge
mumps-mpi 5.2.1 hfd295ca_11 conda-forge
ncurses 6.4 h313beb8_0
nettle 3.7.3 h84b5d62_1
numpy 1.23.5 py310hb93e574_0
numpy-base 1.23.5 py310haf87e8b_0
openblas 0.3.21 openmp_hf78f355_3 conda-forge
openh264 1.8.0 h98b2900_0
openssl 1.1.1t h03a7124_0 conda-forge
packaging 22.0 py310hca03da5_0
parmetis 4.0.3 hefa2a9d_1005 conda-forge
petsc 3.17.3 real_hf852a44_100 conda-forge
petsc4py 3.17.3 real_h09567b2_101 conda-forge
pillow 9.3.0 py310h313beb8_2
pip 22.3.1 py310hca03da5_0
pooch 1.4.0 pyhd3eb1b0_0
proj 7.2.0 heac154c_1
ptscotch 6.0.9 hd02db47_2 conda-forge
pugixml 1.11.4 hc377ac9_1
pycparser 2.21 pyhd3eb1b0_0
pyopenssl 22.0.0 pyhd3eb1b0_0
pysocks 1.7.1 py310hca03da5_0
python 3.10.8 hf452327_0_cpython conda-forge
python_abi 3.10 3_cp310 conda-forge
pyvista 0.38.3 pyhd8ed1ab_0 conda-forge
readline 8.2 h1a28f6b_0
requests 2.28.1 py310hca03da5_0
scalapack 2.2.0 hb170938_1 conda-forge
scooby 0.7.1 pyhd8ed1ab_0 conda-forge
scotch 6.0.9 h7537618_2 conda-forge
setuptools 65.6.3 py310hca03da5_0
slepc 3.17.1 real_h84e8f0d_102 conda-forge
slepc4py 3.17.1 real_hc78d41f_103 conda-forge
snappy 1.1.9 h17c5cce_2 conda-forge
sqlite 3.40.1 h7a7dc30_0
suitesparse 5.10.1 h7cd81ec_1 conda-forge
superlu 5.2.2 hc615359_0 conda-forge
superlu_dist 7.2.0 h7df07b8_0 conda-forge
tbb 2021.7.0 h48ca7d4_0
tbb-devel 2021.7.0 h48ca7d4_0
tk 8.6.12 hb8d0fd4_0
typing_extensions 4.4.0 py310hca03da5_0
tzdata 2022g h04d1e81_0
urllib3 1.26.14 py310hca03da5_0
utfcpp 3.2.1 hca03da5_0
vtk 9.0.3 py310h30f073a_200
wheel 0.38.4 py310hca03da5_0
x264 1!152.20180806 h1a28f6b_0
xtensor 0.24.5 hffc8910_0 conda-forge
xtl 0.7.5 hffc8910_0 conda-forge
xz 5.2.10 h80987f9_1
yaml 0.2.5 h3422bc3_2 conda-forge
zeromq 4.3.4 hbdafb3b_1 conda-forge
zfp 0.5.5 hcfdfaf5_8 conda-forge
zlib 1.2.13 h03a7124_4 conda-forge
zstd 1.5.2 h8574219_0
dokken
February 23, 2023, 2:58pm
7
So it seems like you have installed it in the fenicsx-env. Have you activated it? what is the output of export $PYTHONPATH?
Yes it is activated using:
conda activate fenicsx-env
Here is the output of the export function:
declare -x CONDA_DEFAULT_ENV="fenicsx-env"
declare -x CONDA_EXE="/Users/fwaharte/mambaforge3/bin/conda"
declare -x CONDA_PREFIX="/Users/fwaharte/mambaforge3/envs/fenicsx-env"
declare -x CONDA_PREFIX_1="/Users/fwaharte/mambaforge3"
declare -x CONDA_PROMPT_MODIFIER="(fenicsx-env) "
declare -x CONDA_PYTHON_EXE="/Users/fwaharte/mambaforge3/bin/python"
declare -x CONDA_SHLVL="2"
declare -x GSETTINGS_SCHEMA_DIR="/Users/fwaharte/mambaforge3/envs/fenicsx-env/share/glib-2.0/schemas"
declare -x GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=""
declare -x HOME="/Users/fwaharte"
declare -x HOMEBREW_CELLAR="/opt/homebrew/Cellar"
declare -x HOMEBREW_PREFIX="/opt/homebrew"
declare -x HOMEBREW_REPOSITORY="/opt/homebrew"
declare -x INFOPATH="/opt/homebrew/share/info:"
declare -x JAVA_HOME="/Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents\$"
declare -x LANG="en_GB.UTF-8"
declare -x LOGNAME="fwaharte"
declare -x LaunchInstanceID="F80F7945-79DC-450A-B27A-8C64B29887E2"
declare -x MANPATH="/opt/homebrew/share/man:"
declare -x OLDPWD="/Users/fwaharte"
declare -x PATH="/Applications/FreeFem++.app/Contents/ff-4.11/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Users/fwaharte/mambaforge3/envs/fenicsx-env/bin:/Users/fwaharte/mambaforge3/condabin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin"
declare -x PROJ_DATA="/Users/fwaharte/mambaforge3/envs/fenicsx-env/share/proj"
declare -x PROJ_LIB="/Users/fwaharte/mambaforge3/envs/fenicsx-env/share/proj"
declare -x PROJ_NETWORK="ON"
declare -x PWD="/Users/fwaharte/Downloads"
declare -x SECURITYSESSIONID="186a6"
declare -x SHELL="/bin/bash"
declare -x SHLVL="1"
declare -x SSH_AUTH_SOCK="/private/tmp/com.apple.launchd.ObYr6R9CqO/Listeners"
declare -x TERM="xterm-256color"
declare -x TERM_PROGRAM="Apple_Terminal"
declare -x TERM_PROGRAM_VERSION="447"
declare -x TERM_SESSION_ID="DAD287FD-774A-47B0-B247-0F3D208874F5"
declare -x TMPDIR="/var/folders/nn/3jwzjtl56z91x1sp9yz_fd9r023mdn/T/"
declare -x USER="fwaharte"
declare -x XPC_FLAGS="0x0"
declare -x XPC_SERVICE_NAME="0"
declare -x _CE_CONDA=""
declare -x _CE_M=""
declare -x __CFBundleIdentifier="com.apple.Terminal"
dokken
February 23, 2023, 3:17pm
9
Sorry, i meant echo $PYTHONPATH
dokken:
echo $PYTHONPATH
Oh, ok!
Then the output is empty. Not good I guess…
dokken
February 23, 2023, 6:24pm
11
After activating the environment, there should be a path to the environment in $PYTHONPATH
That’s odd then…
minrk
February 24, 2023, 11:05am
13
I suspect this is a case of python3 not being the Python executable you expect it to be. You might start by checking which python3. You can also try being explicit about using the Python in your environment:
/Users/fwaharte/mambaforge3/envs/fenicsx-env/bin/python3 demo_poisson.py
No, $PYTHONPATH should almost always be undefined. It’s only really used when standard installation is unavailable.
Perhaps you mean the actual import path (to which $PYTHONPATH is one contributor), which would be the output of python3 -m site. At runtime, you can check print(sys.path).
This line:
suggests that the environment isn’t first on your $PATH, which in turn makes me thing that which python3 is going to return /opt/homebrew/bin/python3.
I don’t quite understand why conda activate -n fenicsx-env is not adding the env to the front of your PATH, but that seems to be the root cause. Does a fresh shell help at all?
Does it help to run:
. /Users/myname/opt/anaconda3/etc/profile.d/conda.sh
before running conda activate again?
2 Likes
I tried with a fresh shell: not better.
I ran the command
. /Users/myname/opt/anaconda3/etc/profile.d/conda.sh
But when I want to activate the env, I get this error message:
EnvironmentNameNotFound: Could not find conda environment: fenicsx-env
So I recreated a new env, installed fenicsx using conda.
