RemDelaporteMathurin
commented
2 years ago It seems this issue is similar to https://github.com/conda-forge/fenics-feedstock/issues/87
Closed RemDelaporteMathurin closed 2 years ago
RemDelaporteMathurin
commented
2 years ago It seems this issue is similar to https://github.com/conda-forge/fenics-feedstock/issues/87
RemDelaporteMathurin
commented
2 years ago this is the list of packages on my Windows machine (same docker image) where everything works fine:
_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 21.2.4 py39h06a4308_0
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-forgeAnd this is the environment info:
active environment : base
active env location : /opt/conda
shell level : 1
user config file : /root/.condarc
populated config files :
conda version : 4.13.0
conda-build version : not installed
python version : 3.9.12.final.0
virtual packages : __linux=5.10.16.3=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
/root/.conda/pkgs
envs directories : /opt/conda/envs
/root/.conda/envs
platform : linux-64
user-agent : conda/4.13.0 requests/2.27.1 CPython/3.9.12 Linux/5.10.16.3-microsoft-standard-WSL2 debian/11 glibc/2.31
UID:GID : 0:0
netrc file : None
offline mode : False
minrk
commented
2 years ago Have you activated the env? The compiler packages set $CXX, $CC, and friends on environment activation. If you just installed fenics in the base env, try: conda activate base.
RemDelaporteMathurin
commented
2 years ago try:
conda activate base.
I ran conda activate base but got the following error:
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.Also, when I run this environment (docker image + conda install fenics) in Windows, everything works fine and I don't need to do anything to run fenics
minrk
commented
2 years ago I don't know what's different about your Windows and other docker environment, but that lack of conda init is definitely the key. I'm not sure if it's how the image is being invoked, or if CMD/ENTRYPOINT are being overridden. A complete example of what's being built/run may help.
You can re-enable the conda command with:
source $PREFIX/etc/profile.d/conda.sh
conda activate baseIf you're installing from conda-forge, I might also recommend using the condaforge/mambaforge image. It'll be a bit quicker/lighter since it won't have to replace things from the anaconda channel with the same packages from conda-forge.
minrk
commented
2 years ago Note that the profile.d/conda.sh will only be run by default for interactive shell sessions, but not noninteractive ones. So you may see a difference between:
$ docker run --rm -it my-image bash
[image prompt] $ python fenics-script.py # OK$ docker run --rm -it my-image python fenics-script.py # No such file or directory: 'c++' Ensuring you alwasy invoke an interactive shell:
$ docker run --rm -it my-image bash -i -c "python fenics-script.py"is one way to ensure the shell is fully set up
RemDelaporteMathurin
commented
2 years ago Right so here's what i'm building:
My Dockerfile:
FROM continuumio/miniconda3
RUN conda install -c conda-forge fenics
RUN pip install festim matplotlib meshio[all] ipykernel h-transport-materials==0.4.0I run it locally with
docker build . -t festim-workshop
docker run -ti festim-workshopThen just to test the implementation I run:
python -c "import fenics as f; mesh = f.UnitSquareMesh(3, 3);V = f.FunctionSpace(mesh, 'P', 1)"Locally, everything works fine (no conda init or anything).
What I'm trying to do is having this run in GitHub actions for CI.
My workflow file
jobs:
build:
runs-on: ubuntu-latest
container: remdelaportemathurin/festim-workshop # built from the Dockerfile above
steps:
- uses: actions/checkout@v2
- name: Test fenics
run : |
python -c "import fenics as f; mesh = f.UnitSquareMesh(3, 3);V = f.FunctionSpace(mesh, 'P', 1)"This last step produces this error message:
Run python -c "import fenics as f; mesh = f.UnitSquareMesh(3, 3);V = f.FunctionSpace(mesh, 'P', 1)"
Calling FFC just-in-time (JIT) compiler, this may take some time.
Traceback (most recent call last):
File "<string>", line 1, in <module>
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 [4](https://github.com/RemDelaporteMathurin/FESTIM-workshop/runs/7745477951?check_suite_focus=true#step:4:5)2, 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 130, 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 1[5](https://github.com/RemDelaporteMathurin/FESTIM-workshop/runs/7745477951?check_suite_focus=true#step:4:6)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 1[8](https://github.com/RemDelaporteMathurin/FESTIM-workshop/runs/7745477951?check_suite_focus=true#step:4:9)[21](https://github.com/RemDelaporteMathurin/FESTIM-workshop/runs/7745477951?check_suite_focus=true#step:4:22), in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'c++'
Error: Process completed with exit code 1.When I add conda init bash and conda activate base, the workflow file looks like this:
jobs:
build:
runs-on: ubuntu-latest
container: remdelaportemathurin/festim-workshop
steps:
- uses: actions/checkout@v2
- name: Conda init
run : conda init bash
- name: Test fenics
run : |
conda activate base
python -c "import fenics as f; mesh = f.UnitSquareMesh(3, 3);V = f.FunctionSpace(mesh, 'P', 1)"I get the following error in GA:
Run conda activate base
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
Error: Process completed with exit code 1.The complete workflow can be found here
RemDelaporteMathurin
commented
2 years ago Note that the
profile.d/conda.shwill only be run by default for interactive shell sessions, but not noninteractive ones. So you may see a difference between:$ docker run --rm -it my-image bash [image prompt] $ python fenics-script.py # OK$ docker run --rm -it my-image python fenics-script.py # No such file or directory: 'c++'Ensuring you alwasy invoke an interactive shell:
$ docker run --rm -it my-image bash -i -c "python fenics-script.py"is one way to ensure the shell is fully set up
Thanks for this tip. The problem is I use this image in a Github actions workflow so I don't really know how to do that :-/
minrk
commented
2 years ago Add:
defaults:
run:
# ensure base env is activated when running commands
shell: bash -eo pipefail -c "source /opt/conda/etc/profile.d/conda.sh; conda activate base; source {0}"to your workflow file. This will ensure the conda env is activated before each run command.
RemDelaporteMathurin
commented
2 years ago Yep that fixed it! Thank you very much @minrk
Solution to issue cannot be found in 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:
Everything works fine on my windows machine, but when running on ubuntu it seems that the c++ files are not found:
Full error message here
Here is the github actions file.
Installed packages
Environment info