Hello,
I would like to use RBnics in jupyter notebook in my fenics enviroment but I do not know how to install the module rbnics via conda forget.
How can I use rbnics in jupyter notebook?
Hi,
we do not have an RBniCS conda package. However, following the instructions in our README (https://gitlab.com/RBniCS/RBniCS/-/blob/master/README.md, section 2) should be enough to install RBniCS in your existing environment.
Links to some existing notebooks (running on google colab) are also provided in the README.
Feel free to contact me for any further questions.
Best regards,
Francesco Ballarin
3 Likes
I have installed it in that way in my environment but when i try to call by through from rbnics import * then I get the following error: No module named ‘rbnics’.
However, when I use conda list in my environment I can see that the rbnics is installed
<pre># packages in environment at /home/mondragon/anaconda3/envs/fenics:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
attrs 19.3.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
binutils_impl_linux-64 2.34 h53a641e_0 conda-forge
binutils_linux-64 2.34 hc952b39_18 conda-forge
bleach 3.1.4 pyh9f0ad1d_0 conda-forge
boost-cpp 1.72.0 h8e57a91_0 conda-forge
bzip2 1.0.8 h516909a_2 conda-forge
ca-certificates 2020.6.20 hecda079_0 conda-forge
certifi 2020.6.20 py38h32f6830_0 conda-forge
cftime 1.1.1 py38h8790de6_0 conda-forge/label/cf202003
cloudpickle 1.3.0 py_0
cmake 3.17.0 h28c56e5_0 conda-forge
curl 7.68.0 hf8cf82a_0 conda-forge/label/cf202003
cvxopt 1.2.5 pypi_0 pypi
cycler 0.10.0 py_2 conda-forge
dbus 1.13.6 he372182_0 conda-forge
decorator 4.4.2 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
eigen 3.3.7 hc9558a2_1001 conda-forge
entrypoints 0.3 py38h32f6830_1001 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
fastcache 1.1.0 py38h1e0a361_1 conda-forge
fenics 2019.1.0 py38_9 conda-forge
fenics-dijitso 2019.1.0 py_9 conda-forge
fenics-dolfin 2019.1.0 py38ha98eaef_9 conda-forge
fenics-ffc 2019.1.0 py_9 conda-forge
fenics-fiat 2019.1.0 py_9 conda-forge
fenics-libdolfin 2019.1.0 h24fb424_9 conda-forge
fenics-ufl 2019.1.0 py_9 conda-forge
fontconfig 2.13.1 h86ecdb6_1001 conda-forge
freetype 2.10.1 he06d7ca_0 conda-forge
gcc_impl_linux-64 7.3.0 hd420e75_5 conda-forge
gcc_linux-64 7.3.0 h553295d_18 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
glib 2.64.2 h6f030ca_0 conda-forge
gmp 6.2.0 he1b5a44_2 conda-forge
gmpy2 2.1.0b1 py38h04dde30_0 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
gxx_impl_linux-64 7.3.0 hdf63c60_5 conda-forge
gxx_linux-64 7.3.0 h553295d_18 conda-forge
h5py 2.10.0 nompi_py38h513d04c_102 conda-forge/label/cf202003
hdf4 4.2.13 hf30be14_1003 conda-forge/label/cf202003
hdf5 1.10.5 mpi_mpich_ha7d0aea_1004 conda-forge
hypre 2.18.2 hc98498a_1 conda-forge
icu 64.2 he1b5a44_1 conda-forge
importlib-metadata 1.6.0 py38h32f6830_0 conda-forge
importlib_metadata 1.6.0 0 conda-forge
ipykernel 5.2.0 py38h23f93f0_1 conda-forge
ipython 7.13.0 py38h32f6830_2 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jedi 0.17.0 py38h32f6830_0 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
jsonschema 3.2.0 py38h32f6830_1 conda-forge
jupyter_client 6.1.3 py_0 conda-forge
jupyter_contrib_core 0.3.3 py_2 conda-forge
jupyter_contrib_nbextensions 0.5.1 py38_0 conda-forge
jupyter_core 4.6.3 py38h32f6830_1 conda-forge
jupyter_highlight_selected_word 0.2.0 py38_1000 conda-forge
jupyter_latex_envs 1.4.6 py38_1000 conda-forge
jupyter_nbextensions_configurator 0.4.1 py38_0 conda-forge
kiwisolver 1.2.0 py38hbf85e49_0 conda-forge
krb5 1.16.4 h2fd8d38_0 conda-forge/label/cf202003
ld_impl_linux-64 2.34 h53a641e_0 conda-forge
libblas 3.8.0 16_openblas conda-forge
libcblas 3.8.0 16_openblas conda-forge
libclang 9.0.1 default_hde54327_0 conda-forge
libcurl 7.68.0 hda55be3_0 conda-forge/label/cf202003
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.3.0 hdf63c60_5 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
libiconv 1.15 h516909a_1006 conda-forge
liblapack 3.8.0 16_openblas conda-forge
libllvm9 9.0.1 he513fc3_1 conda-forge
libnetcdf 4.7.3 mpi_mpich_h755db7c_1 conda-forge/label/cf202003
libopenblas 0.3.9 h5ec1e0e_0 conda-forge
libpng 1.6.37 hed695b0_1 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libuv 1.34.0 h516909a_0 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxkbcommon 0.10.0 he1b5a44_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
libxslt 1.1.33 h31b3aaa_0 conda-forge
llvm-openmp 10.0.0 hc9558a2_0 conda-forge
lxml 4.5.0 py38hbb43d70_1 conda-forge
markupsafe 1.1.1 py38h1e0a361_1 conda-forge
matplotlib 3.2.1 0 conda-forge
matplotlib-base 3.2.1 py38h2af1d28_0 conda-forge
meshio 4.0.4 py_0 conda-forge/label/cf202003
metis 5.1.0 he1b5a44_1005 conda-forge
mistune 0.8.4 py38h1e0a361_1001 conda-forge
mpc 1.1.0 h04dde30_1007 conda-forge
mpfr 4.0.2 he80fd80_1 conda-forge
mpi 1.0 mpich conda-forge
mpi4py 3.0.3 py38h4a80816_1 conda-forge
mpich 3.3.2 hc856adb_0 conda-forge
mpmath 1.1.0 pypi_0 pypi
mshr 2019.1.0 py38hf9f41d3_3 conda-forge
multipledispatch 0.6.0 pypi_0 pypi
mumps-include 5.2.1 6 conda-forge
mumps-mpi 5.2.1 h645f208_6 conda-forge
nbconvert 5.6.1 py38h32f6830_1 conda-forge
nbformat 5.0.6 py_0 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
netcdf4 1.5.3 mpi_mpich_py38h00fb2e7_2 conda-forge/label/cf202003
notebook 6.0.3 py38_0 conda-forge
nspr 4.25 he1b5a44_0 conda-forge
nss 3.47 he751ad9_0 conda-forge
numpy 1.18.1 py38h8854b6b_1 conda-forge
openssl 1.1.1g h516909a_1 conda-forge
pandoc 2.9.2.1 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parmetis 4.0.3 h9f7b9cf_1005 conda-forge
parso 0.7.0 pyh9f0ad1d_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
petsc 3.12.4 h432f2ec_0 conda-forge
petsc4py 3.12.0 py38h30bdb2a_4 conda-forge
pexpect 4.8.0 py38h32f6830_1 conda-forge
pickleshare 0.7.5 py38h32f6830_1001 conda-forge
pip 20.0.2 py_2 conda-forge
pkg-config 0.29.2 h516909a_1006 conda-forge
pkgconfig 1.4.0 py38h32f6830_0 conda-forge
prometheus_client 0.7.1 py_0 conda-forge
prompt-toolkit 3.0.5 py_0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptscotch 6.0.8 he9f2703_1 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
pybind11 2.4.3 py38hbf85e49_3 conda-forge
pygments 2.6.1 py_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyqt 5.12.3 py38hcca6a23_1 conda-forge
pyqt5-sip 4.19.18 pypi_0 pypi
pyqtwebengine 5.12.1 pypi_0 pypi
pyrsistent 0.16.0 py38h1e0a361_0 conda-forge
pytest-runner 5.2 pypi_0 pypi
python 3.8.2 he5300dc_6_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.8 1_cp38 conda-forge
pyyaml 5.3.1 py38h1e0a361_0 conda-forge
pyzmq 19.0.0 py38ha71036d_1 conda-forge
qt 5.12.5 hd8c4c69_1 conda-forge
rbnics 0.1.dev1 pypi_0 pypi
readline 8.0 hf8c457e_0 conda-forge
rhash 1.3.6 h14c3975_1001 conda-forge
scalapack 2.0.2 hfacbc1e_1008 conda-forge
scipy 1.4.1 py38h18bccfc_3 conda-forge
scotch 6.0.8 h0eec0ba_1 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 46.1.3 py38h32f6830_0 conda-forge
six 1.14.0 py_1 conda-forge
slepc 3.12.2 h76dbdef_0 conda-forge
slepc4py 3.12.0 py38hb2ee469_1 conda-forge
spyder-kernels 0.5.2 py38_0
sqlite 3.30.1 hcee41ef_0 conda-forge
suitesparse 5.6.0 h717dc36_0 conda-forge
superlu 5.2.1 hfe2efc7_1207 conda-forge
superlu_dist 6.2.0 h5e15a89_2 conda-forge
sympy 1.5.1 py38h32f6830_3 conda-forge
tbb 2020.1 hc9558a2_0 conda-forge
terminado 0.8.3 py38h32f6830_1 conda-forge
testpath 0.4.4 py_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
toposort 1.5 pypi_0 pypi
tornado 6.0.4 py38h1e0a361_1 conda-forge
traitlets 4.3.3 py38h32f6830_1 conda-forge
wcwidth 0.1.9 pyh9f0ad1d_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.34.2 py_1 conda-forge
wurlitzer 2.0.0 py38_0
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xz 5.2.5 h516909a_0 conda-forge
yaml 0.2.4 h516909a_0 conda-forge
zeromq 4.3.2 he1b5a44_2 conda-forge
zipp 3.1.0 py_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge</pre>```Please send me a step by step procedure to install the FEniCS conda env from a clean environment, and also add the lines you used to install RBniCS. In this way, I will try to reproduce this on my machine.
I follow the next steps
conda create -n fenics -c conda-forge fenics mshr
conda install -n fenics -c conda-forge ipython notebook matplotlib scipy
conda install -n fenics -c conda-forge meshio petsc slepc petsc4py slepc4py
conda activate fenics
git clone https://gitlab.com/RBniCS/RBniCS.git
python3 'folderpath/setup.py' install
I think that it is all made in my environment
I am afraid that there is something else going on with your environment.
I followed your steps (with the only minor difference
git clone https://gitlab.com/RBniCS/RBniCS.git
cd RBniCS
python3 setup.py install
but that should not affect the installation process) and I can import the library and run the tutorials.
I have installed a new environment and it is working now I guess that there are something wrong with the previous one.
Thank you so much for answer my question, I really appreciate it