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pyiron / pyiron_atomistics

pyiron_atomistics - an integrated development environment (IDE) for atomistic simulation in computational materials science.
https://pyiron-atomistics.readthedocs.io
BSD 3-Clause "New" or "Revised" License
42 stars 15 forks source link

Sphinx examplary notebook fails #379

Closed max-hassani closed 2 years ago

max-hassani commented 2 years ago

I am testing sphinx notebook (the notebook available in pyiron_atomistic repo) on one of pyiron docker images. The job.run() fails with the following error:

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
/tmp/ipykernel_35/567186773.py in <module>
      2 job.structure = pr.create_structure('Fe', 'bcc', a_Fe)
      3 job.calc_static()
----> 4 job.run()

/opt/conda/lib/python3.9/site-packages/pyiron_base/generic/util.py in decorated(*args, **kwargs)
    211                         stacklevel=2
    212                     )
--> 213             return function(*args, **kwargs)
    214         return decorated
    215 

/opt/conda/lib/python3.9/site-packages/pyiron_base/job/generic.py in run(self, delete_existing_job, repair, debug, run_mode, run_again)
    666                 self._run_if_repair()
    667             elif status == "initialized":
--> 668                 self._run_if_new(debug=debug)
    669             elif status == "created":
    670                 self._run_if_created()

/opt/conda/lib/python3.9/site-packages/pyiron_base/job/generic.py in _run_if_new(self, debug)
   1320         else:
   1321             self.save()
-> 1322             self.run()
   1323 
   1324     def _run_if_created(self):

/opt/conda/lib/python3.9/site-packages/pyiron_base/generic/util.py in decorated(*args, **kwargs)
    211                         stacklevel=2
    212                     )
--> 213             return function(*args, **kwargs)
    214         return decorated
    215 

/opt/conda/lib/python3.9/site-packages/pyiron_base/job/generic.py in run(self, delete_existing_job, repair, debug, run_mode, run_again)
    668                 self._run_if_new(debug=debug)
    669             elif status == "created":
--> 670                 self._run_if_created()
    671             elif status == "submitted":
    672                 self._run_if_submitted()

/opt/conda/lib/python3.9/site-packages/pyiron_base/job/generic.py in _run_if_created(self)
   1337             self.run_if_manually()
   1338         elif self.server.run_mode.modal:
-> 1339             self.run_static()
   1340         elif self.server.run_mode.non_modal or self.server.run_mode.thread:
   1341             self.run_if_non_modal()

/opt/conda/lib/python3.9/site-packages/pyiron_base/job/generic.py in run_static(self)
    763             "{}, status: {}, output: {}".format(self.job_info_str, self.status, out)
    764         )
--> 765         self.run()
    766         if job_crashed:
    767             self.status.aborted = True

/opt/conda/lib/python3.9/site-packages/pyiron_base/generic/util.py in decorated(*args, **kwargs)
    211                         stacklevel=2
    212                     )
--> 213             return function(*args, **kwargs)
    214         return decorated
    215 

/opt/conda/lib/python3.9/site-packages/pyiron_base/job/generic.py in run(self, delete_existing_job, repair, debug, run_mode, run_again)
    674                 self._run_if_running()
    675             elif status == "collect":
--> 676                 self._run_if_collect()
    677             elif status == "suspend":
    678                 self._run_if_suspended()

/opt/conda/lib/python3.9/site-packages/pyiron_base/job/generic.py in _run_if_collect(self)
   1417         status is set to 'finished'
   1418         """
-> 1419         self.collect_output()
   1420         self.collect_logfiles()
   1421         if self.job_id is not None:

/opt/conda/lib/python3.9/site-packages/pyiron_atomistics/sphinx/interactive.py in collect_output(self, force_update, compress_files)
    215 
    216     def collect_output(self, force_update=False, compress_files=True):
--> 217         super(SphinxInteractive, self).collect_output(force_update=force_update, compress_files=compress_files)
    218         self._output_interactive_to_generic()
    219 

/opt/conda/lib/python3.9/site-packages/pyiron_atomistics/sphinx/base.py in collect_output(self, force_update, compress_files)
   1364         Collects the outputs and stores them to the hdf file
   1365         """
-> 1366         self._output_parser.collect(directory=self.working_directory)
   1367         self._output_parser.to_hdf(self._hdf5, force_update=force_update)
   1368         if compress_files:

/opt/conda/lib/python3.9/site-packages/pyiron_atomistics/sphinx/base.py in collect(self, directory)
   2335             directory (str): the directory to collect the output from.
   2336         """
-> 2337         self.collect_sphinx_log(file_name="sphinx.log", cwd=directory)
   2338         self.collect_energy_dat(file_name="energy.dat", cwd=directory)
   2339         self.collect_residue_dat(file_name="residue.dat", cwd=directory)

/opt/conda/lib/python3.9/site-packages/pyiron_atomistics/sphinx/base.py in collect_sphinx_log(self, file_name, cwd, check_consistency)
   2091             if not np.any(["Enter Main Loop" in line for line in log_file]):
   2092                 self._job.status.aborted = True
-> 2093                 raise AssertionError("SPHInX did not enter the main loop; \
   2094                     output not collected")
   2095             if not np.any(["Program exited normally." in line

AssertionError: SPHInX did not enter the main loop;                     output not collected

Further details of the error can be found here The relevant installed conda packages are listed below:

pyiron                    0.4.5              pyhd8ed1ab_0    conda-forge
pyiron-data               0.0.16               hd8ed1ab_0    conda-forge
pyiron_atomistics         0.2.26             pyhd8ed1ab_0    conda-forge
pyiron_base               0.3.5              pyhd8ed1ab_0    conda-forge
sphinxdft                 3.0.3                h7f852f6_1    conda-forge
sphinxdft-data            0.0.1                hd8ed1ab_2    conda-forge

I do not have enough experience with Sphinx simulations, and I do not know why Sphinx does not enter the main loop. So I would be grateful if anyone has an idea which could help.

samwaseda commented 2 years ago

Yeah I also noticed the same problem some time ago. I'm gonna look into it now.

samwaseda commented 2 years ago

Sorry I just realized that the problem I was talking about was a different one. I guess the one that you raised here is a recurring issue that @jan-janssen mentioned some time ago (cf. this issue)

max-hassani commented 2 years ago

@samwaseda thanks for looking at this problem. The issue occurs by Sphinx-dft=3.0.3, while lower versions (2.7*) was fine. I think something is broken in the latest update :(

max-hassani commented 2 years ago

@freyso, below you can find the pyiron.log:

2021-10-04 16:31:45,065 - pyiron_log - INFO - run job: spx_Fe_nonmag id: None, status: initialized
2021-10-04 16:31:45,065 - pyiron_log - INFO - run job: spx_Fe_nonmag id: None, status: initialized
2021-10-04 16:31:45,808 - pyiron_log - INFO - run job: spx_Fe_nonmag id: 1, status: created
2021-10-04 16:31:45,808 - pyiron_log - INFO - run job: spx_Fe_nonmag id: 1, status: created
2021-10-04 16:31:45,817 - pyiron_log - INFO - job: spx_Fe_nonmag id: 1, status: submitted, run job (modal)
2021-10-04 16:31:45,817 - pyiron_log - INFO - job: spx_Fe_nonmag id: 1, status: submitted, run job (modal)
2021-10-04 16:31:45,883 - pyiron_log - INFO - job: spx_Fe_nonmag id: 1, status: collect, output: sphinx: error while loading shared libraries: libmkl_intel_lp64.so.1: cannot open shared object file: No such file or directory
sphinx: error while loading shared libraries: libmkl_intel_lp64.so.1: cannot open shared object file: No such file or directory

2021-10-04 16:31:45,883 - pyiron_log - INFO - job: spx_Fe_nonmag id: 1, status: collect, output: sphinx: error while loading shared libraries: libmkl_intel_lp64.so.1: cannot open shared object file: No such file or directory
sphinx: error while loading shared libraries: libmkl_intel_lp64.so.1: cannot open shared object file: No such file or directory

2021-10-04 16:31:45,883 - pyiron_log - INFO - run job: spx_Fe_nonmag id: 1, status: collect
2021-10-04 16:31:45,883 - pyiron_log - INFO - run job: spx_Fe_nonmag id: 1, status: collect

The error.out also shows similar error:

sphinx: error while loading shared libraries: libmkl_intel_lp64.so.1: cannot open shared object file: No such file or directory
sphinx: error while loading shared libraries: libmkl_intel_lp64.so.1: cannot open shared object file: No such file or directory
max-hassani commented 2 years ago

For completeness, I have brought below the output of conda list in the container:

_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
aimsgb                    0.1.0              pyhd8ed1ab_1    conda-forge
alembic                   1.7.3              pyhd8ed1ab_0    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
anyio                     3.3.0            py39hf3d152e_0    conda-forge
argon2-cffi               20.1.0           py39h3811e60_2    conda-forge
ase                       3.22.0             pyhd8ed1ab_0    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     21.2.0             pyhd8ed1ab_0    conda-forge
babel                     2.9.1              pyh44b312d_0    conda-forge
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
bcrypt                    3.2.0            py39h3811e60_1    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
blinker                   1.4                        py_1    conda-forge
blosc                     1.21.0               h9c3ff4c_0    conda-forge
brotlipy                  0.7.0           py39h3811e60_1001    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
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2021.5.30        py39hf3d152e_0    conda-forge
certipy                   0.1.3                      py_0    conda-forge
cffi                      1.14.6           py39he32792d_0    conda-forge
cftime                    1.5.1            py39hce5d2b2_0    conda-forge
chardet                   4.0.0            py39hf3d152e_1    conda-forge
charset-normalizer        2.0.0              pyhd8ed1ab_0    conda-forge
click                     8.0.1            py39hf3d152e_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
conda                     4.10.3           py39hf3d152e_2    conda-forge
conda-package-handling    1.7.3            py39h3811e60_0    conda-forge
configurable-http-proxy   4.5.0           node15_he6ea98c_0    conda-forge
cryptography              3.4.7            py39hbca0aa6_0    conda-forge
curl                      7.79.1               hea6ffbf_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
dbus                      1.13.6               h48d8840_2    conda-forge
debugpy                   1.4.1            py39he80948d_0    conda-forge
decorator                 5.1.0              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dill                      0.3.4              pyhd8ed1ab_0    conda-forge
double-conversion         3.1.5                h9c3ff4c_2    conda-forge
eigen                     3.4.0                h4bd325d_0    conda-forge
entrypoints               0.3             py39hde42818_1002    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
f90wrap                   0.2.7            py39h984b4d8_0    conda-forge
ffmpeg                    4.3.2                hca11adc_0    conda-forge
fftw                      3.3.10          nompi_h74d3f13_101    conda-forge
flask                     2.0.1              pyhd8ed1ab_0    conda-forge
fontconfig                2.13.1            hba837de_1005    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
future                    0.18.2           py39hf3d152e_3    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
git                       2.33.0          pl5321hc30692c_1    conda-forge
gitdb                     4.0.7              pyhd8ed1ab_0    conda-forge
gitpython                 3.1.24             pyhd8ed1ab_0    conda-forge
gl2ps                     1.4.2                h0708190_0    conda-forge
glew                      2.1.0                h9c3ff4c_2    conda-forge
glib                      2.68.4               h9c3ff4c_0    conda-forge
glib-tools                2.68.4               h9c3ff4c_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmpy2                     2.1.0b5          py39h78fa15d_0    conda-forge
gnutls                    3.6.13               h85f3911_1    conda-forge
gpaw                      21.6.0           py39_openmpi_1    conda-forge
gpaw-data                 0.9.20000                     0    conda-forge
greenlet                  1.1.1            py39he80948d_0    conda-forge
gsl                       2.6                  he838d99_2    conda-forge
gst-plugins-base          1.18.5               hf529b03_0    conda-forge
gstreamer                 1.18.5               h76c114f_0    conda-forge
h5io                      0.1.2              pyh95af2a2_0    conda-forge
h5py                      3.3.0           nompi_py39h98ba4bc_100    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.10.6          nompi_h6a2412b_1114    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
idna                      3.1                pyhd3deb0d_0    conda-forge
importlib-metadata        4.8.1            py39hf3d152e_0    conda-forge
importlib_metadata        4.8.1                hd8ed1ab_0    conda-forge
importlib_resources       5.2.2              pyhd8ed1ab_0    conda-forge
iprpy-data                2021.2.23          pyh44b312d_0    conda-forge
ipykernel                 6.4.1            py39hef51801_0    conda-forge
ipython                   7.27.0           py39hef51801_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.5              pyhd8ed1ab_0    conda-forge
itsdangerous              2.0.1              pyhd8ed1ab_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.0           py39hf3d152e_2    conda-forge
jinja2                    3.0.1              pyhd8ed1ab_0    conda-forge
joblib                    1.0.1              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsoncpp                   1.9.4                h4bd325d_3    conda-forge
jsonschema                3.2.0              pyhd8ed1ab_3    conda-forge
jupyter_client            7.0.3              pyhd8ed1ab_0    conda-forge
jupyter_core              4.8.1            py39hf3d152e_0    conda-forge
jupyter_server            1.11.0             pyhd8ed1ab_0    conda-forge
jupyter_telemetry         0.1.0              pyhd8ed1ab_1    conda-forge
jupyterhub                1.4.2            py39hf3d152e_0    conda-forge
jupyterhub-base           1.4.2            py39hf3d152e_0    conda-forge
jupyterlab                3.1.13             pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_server         2.8.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.0.2              pyhd8ed1ab_0    conda-forge
kim-api                   2.2.1                h5c8ed42_0    conda-forge
kiwisolver                1.3.2            py39h1a9c180_0    conda-forge
krb5                      1.19.2               hcc1bbae_1    conda-forge
lame                      3.100             h7f98852_1001    conda-forge
lammps                    2021.07.30      py39h910f28c_openmpi_1    conda-forge
latexcodec                2.0.1              pyh9f0ad1d_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
libarchive                3.5.2                hccf745f_1    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                   7.79.1               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                    3.3                  h58526e2_2    conda-forge
libgcc-ng                 11.2.0               h1d223b6_8    conda-forge
libgfortran-ng            11.2.0               h69a702a_9    conda-forge
libgfortran5              11.2.0               h5c6108e_9    conda-forge
libglib                   2.68.4               h3e27bee_0    conda-forge
libglu                    9.0.0             he1b5a44_1001    conda-forge
libgomp                   11.2.0               h1d223b6_8    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libidn2                   2.3.2                h7f98852_0    conda-forge
liblapack                 3.9.0           11_linux64_openblas    conda-forge
libllvm11                 11.1.0               hf817b99_2    conda-forge
libnetcdf                 4.8.1           nompi_hcd642e3_100    conda-forge
libnghttp2                1.43.0               h812cca2_1    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
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsolv                   0.7.19               h780b84a_5    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              11.2.0               he4da1e4_8    conda-forge
libtheora                 1.1.1             h7f98852_1005    conda-forge
libtiff                   4.3.0                hf544144_1    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libuv                     1.41.1               h7f98852_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.2.1                h7f98852_0    conda-forge
libxc                     4.3.4                h86c2bf4_2    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
libzip                    1.8.0                h4de3113_1    conda-forge
llvm-openmp               12.0.1               h4bd325d_1    conda-forge
loguru                    0.5.3            py39hf3d152e_2    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mako                      1.1.5              pyhd8ed1ab_0    conda-forge
mamba                     0.15.3           py39h951de11_0    conda-forge
markupsafe                2.0.1            py39h3811e60_0    conda-forge
matplotlib-base           3.4.3            py39h2fa2bec_1    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mendeleev                 0.9.0              pyh8a188c0_0    conda-forge
mistune                   0.8.4           py39h3811e60_1004    conda-forge
mkl                       2020.4             h726a3e6_304    conda-forge
mlip                      1.0                  hf1f3868_2    conda-forge
mock                      4.0.3            py39hf3d152e_1    conda-forge
monty                     2021.8.17          pyhd8ed1ab_0    conda-forge
mpc                       1.2.1                h9f54685_0    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
mpi                       1.0                     openmpi    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
mysql-common              8.0.25               ha770c72_2    conda-forge
mysql-libs                8.0.25               hfa10184_2    conda-forge
n2p2                      2.1.1            py39hccc7027_0    conda-forge
nbclassic                 0.3.2              pyhd8ed1ab_0    conda-forge
nbclient                  0.5.4              pyhd8ed1ab_0    conda-forge
nbconvert                 6.2.0            py39hf3d152e_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
netcdf4                   1.5.7           nompi_py39hd2e3950_101    conda-forge
nettle                    3.6                  he412f7d_0    conda-forge
networkx                  2.5                        py_0    conda-forge
nglview                   3.0.3              pyh8a188c0_0    conda-forge
nodejs                    15.14.0              h92b4a50_0    conda-forge
notebook                  6.4.4              pyha770c72_0    conda-forge
nspr                      4.30                 h9c3ff4c_0    conda-forge
nss                       3.69                 hb5efdd6_1    conda-forge
numexpr                   2.7.3            py39hde0f152_0    conda-forge
numpy                     1.21.2           py39hdbf815f_0    conda-forge
oauthlib                  3.1.1              pyhd8ed1ab_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openh264                  2.1.1                h780b84a_0    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openkim-models            2021.01.28           h2cc385e_1    conda-forge
openmpi                   4.1.1                hbfc84c5_0    conda-forge
openssl                   1.1.1l               h7f98852_0    conda-forge
packaging                 21.0               pyhd8ed1ab_0    conda-forge
palettable                3.3.0                      py_0    conda-forge
pamela                    1.0.0                      py_0    conda-forge
pandas                    1.3.3            py39hde0f152_0    conda-forge
pandoc                    2.14.2               h7f98852_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
paramiko                  2.7.2              pyh9f0ad1d_0    conda-forge
parso                     0.8.2              pyhd8ed1ab_0    conda-forge
pathlib2                  2.3.6            py39hf3d152e_0    conda-forge
patsy                     0.5.2              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.37                h032f7d1_0    conda-forge
perl                      5.32.1          0_h7f98852_perl5    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
phonopy                   2.11.0           py39hce5d2b2_1    conda-forge
pickleshare               0.7.5           py39hde42818_1002    conda-forge
pillow                    8.3.2            py39ha612740_0    conda-forge
pint                      0.17               pyhd8ed1ab_1    conda-forge
pip                       21.2.4             pyhd8ed1ab_0    conda-forge
pkg-config                0.29.2            h36c2ea0_1008    conda-forge
plotly                    5.3.1              pyhd8ed1ab_0    conda-forge
proj                      8.1.0                h277dcde_1    conda-forge
prometheus_client         0.11.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.20             pyha770c72_0    conda-forge
psutil                    5.8.0            py39h3811e60_1    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pugixml                   1.11.4               h9c3ff4c_0    conda-forge
pybtex                    0.24.0           py39hf3d152e_0    conda-forge
pycosat                   0.6.3           py39h3811e60_1006    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pycurl                    7.44.1           py39h72e3413_0    conda-forge
pyfiglet                  0.8.post1                  py_0    conda-forge
pyfileindex               0.0.6              pyhd8ed1ab_0    conda-forge
pygments                  2.10.0             pyhd8ed1ab_0    conda-forge
pyiron                    0.4.5              pyhd8ed1ab_0    conda-forge
pyiron-data               0.0.16               hd8ed1ab_0    conda-forge
pyiron_atomistics         0.2.26             pyhd8ed1ab_0    conda-forge
pyiron_base               0.3.5              pyhd8ed1ab_0    conda-forge
pyjwt                     2.1.0              pyhd8ed1ab_0    conda-forge
pymatgen                  2022.0.14        py39h1a9c180_0    conda-forge
pynacl                    1.4.0            py39h3811e60_2    conda-forge
pyopenssl                 20.0.1             pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyrsistent                0.17.3           py39h3811e60_2    conda-forge
pyscal                    2.10.14          py39h5472131_1    conda-forge
pysocks                   1.7.1            py39hf3d152e_3    conda-forge
pysqa                     0.0.15             pyhd8ed1ab_0    conda-forge
pytables                  3.6.1            py39hf6dc253_3    conda-forge
python                    3.9.6           h49503c6_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.1              pyh9f0ad1d_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytz                      2021.1             pyhd8ed1ab_0    conda-forge
pyyaml                    5.4.1            py39h3811e60_1    conda-forge
pyzmq                     22.3.0           py39h37b5a0c_0    conda-forge
qt                        5.12.9               hda022c4_4    conda-forge
quippy                    0.0.1            py39hbb6cefa_2    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
reproc                    14.2.3               h7f98852_0    conda-forge
reproc-cpp                14.2.3               h9c3ff4c_0    conda-forge
requests                  2.26.0             pyhd8ed1ab_0    conda-forge
requests-unixsocket       0.2.0                      py_0    conda-forge
ruamel.yaml               0.17.16          py39h3811e60_0    conda-forge
ruamel.yaml.clib          0.2.2            py39h3811e60_2    conda-forge
ruamel_yaml               0.15.80         py39h3811e60_1004    conda-forge
scalapack                 2.0.2             hc7fdd6d_1009    conda-forge
scandir                   1.10.0           py39h3811e60_3    conda-forge
scikit-learn              1.0              py39h7c5d8c9_1    conda-forge
scipy                     1.7.1            py39hee8e79c_0    conda-forge
seaborn                   0.11.2               hd8ed1ab_0    conda-forge
seaborn-base              0.11.2             pyhd8ed1ab_0    conda-forge
seekpath                  2.0.1              pyh44b312d_1    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                58.0.4           py39hf3d152e_2    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
sniffio                   1.2.0            py39hf3d152e_1    conda-forge
spglib                    1.16.2           py39hce5d2b2_0    conda-forge
sphinxdft                 3.0.3                h7f852f6_1    conda-forge
sphinxdft-data            0.0.1                hd8ed1ab_2    conda-forge
sqlalchemy                1.4.25           py39h3811e60_0    conda-forge
sqlite                    3.36.0               h9cd32fc_2    conda-forge
statsmodels               0.12.2           py39hce5d2b2_0    conda-forge
sympy                     1.8              py39hf3d152e_0    conda-forge
tabulate                  0.8.9              pyhd8ed1ab_0    conda-forge
tbb                       2020.2               h4bd325d_4    conda-forge
tbb-devel                 2020.2               h4bd325d_4    conda-forge
tenacity                  8.0.1              pyhd8ed1ab_0    conda-forge
terminado                 0.12.1           py39hf3d152e_0    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             2.2.0              pyh8a188c0_0    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
tornado                   6.1              py39h3811e60_1    conda-forge
tqdm                      4.62.3             pyhd8ed1ab_0    conda-forge
traitlets                 5.1.0              pyhd8ed1ab_0    conda-forge
typing_extensions         3.10.0.2           pyha770c72_0    conda-forge
tzdata                    2021a                he74cb21_1    conda-forge
uncertainties             3.1.6              pyhd8ed1ab_0    conda-forge
urllib3                   1.26.7             pyhd8ed1ab_0    conda-forge
utfcpp                    3.2.1                ha770c72_0    conda-forge
vtk                       9.0.3           no_osmesa_py39hb68e339_103    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          0.57.0           py39hf3d152e_4    conda-forge
werkzeug                  2.0.1              pyhd8ed1ab_0    conda-forge
wget                      1.20.3               ha56f1ee_1    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        3.5.1            py39hf3d152e_4    conda-forge
x264                      1!161.3030           h7f98852_1    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h516909a_0    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.5.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge
jan-janssen commented 2 years ago

Can you compare it to the environment used during the notebook tests?

On Mon, Oct 4, 2021, 10:39 AM MuhammadHassani @.***> wrote:

For completeness, I have brought below the output of conda list:

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_llvm conda-forge aimsgb 0.1.0 pyhd8ed1ab_1 conda-forge alembic 1.7.3 pyhd8ed1ab_0 conda-forge alsa-lib 1.2.3 h516909a_0 conda-forge anyio 3.3.0 py39hf3d152e_0 conda-forge argon2-cffi 20.1.0 py39h3811e60_2 conda-forge ase 3.22.0 pyhd8ed1ab_0 conda-forge async_generator 1.10 py_0 conda-forge attrs 21.2.0 pyhd8ed1ab_0 conda-forge babel 2.9.1 pyh44b312d_0 conda-forge 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 bcrypt 3.2.0 py39h3811e60_1 conda-forge bleach 4.1.0 pyhd8ed1ab_0 conda-forge blinker 1.4 py_1 conda-forge blosc 1.21.0 h9c3ff4c_0 conda-forge brotlipy 0.7.0 py39h3811e60_1001 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 cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge certifi 2021.5.30 py39hf3d152e_0 conda-forge certipy 0.1.3 py_0 conda-forge cffi 1.14.6 py39he32792d_0 conda-forge cftime 1.5.1 py39hce5d2b2_0 conda-forge chardet 4.0.0 py39hf3d152e_1 conda-forge charset-normalizer 2.0.0 pyhd8ed1ab_0 conda-forge click 8.0.1 py39hf3d152e_0 conda-forge colorama 0.4.4 pyh9f0ad1d_0 conda-forge conda 4.10.3 py39hf3d152e_2 conda-forge conda-package-handling 1.7.3 py39h3811e60_0 conda-forge configurable-http-proxy 4.5.0 node15_he6ea98c_0 conda-forge cryptography 3.4.7 py39hbca0aa6_0 conda-forge curl 7.79.1 hea6ffbf_0 conda-forge cycler 0.10.0 py_2 conda-forge dataclasses 0.8 pyhc8e2a94_3 conda-forge dbus 1.13.6 h48d8840_2 conda-forge debugpy 1.4.1 py39he80948d_0 conda-forge decorator 5.1.0 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge dill 0.3.4 pyhd8ed1ab_0 conda-forge double-conversion 3.1.5 h9c3ff4c_2 conda-forge eigen 3.4.0 h4bd325d_0 conda-forge entrypoints 0.3 py39hde42818_1002 conda-forge expat 2.4.1 h9c3ff4c_0 conda-forge f90wrap 0.2.7 py39h984b4d8_0 conda-forge ffmpeg 4.3.2 hca11adc_0 conda-forge fftw 3.3.10 nompi_h74d3f13_101 conda-forge flask 2.0.1 pyhd8ed1ab_0 conda-forge fontconfig 2.13.1 hba837de_1005 conda-forge freetype 2.10.4 h0708190_1 conda-forge future 0.18.2 py39hf3d152e_3 conda-forge gettext 0.19.8.1 h0b5b191_1005 conda-forge git 2.33.0 pl5321hc30692c_1 conda-forge gitdb 4.0.7 pyhd8ed1ab_0 conda-forge gitpython 3.1.24 pyhd8ed1ab_0 conda-forge gl2ps 1.4.2 h0708190_0 conda-forge glew 2.1.0 h9c3ff4c_2 conda-forge glib 2.68.4 h9c3ff4c_0 conda-forge glib-tools 2.68.4 h9c3ff4c_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge gmpy2 2.1.0b5 py39h78fa15d_0 conda-forge gnutls 3.6.13 h85f3911_1 conda-forge gpaw 21.6.0 py39_openmpi_1 conda-forge gpaw-data 0.9.20000 0 conda-forge greenlet 1.1.1 py39he80948d_0 conda-forge gsl 2.6 he838d99_2 conda-forge gst-plugins-base 1.18.5 hf529b03_0 conda-forge gstreamer 1.18.5 h76c114f_0 conda-forge h5io 0.1.2 pyh95af2a2_0 conda-forge h5py 3.3.0 nompi_py39h98ba4bc_100 conda-forge hdf4 4.2.15 h10796ff_3 conda-forge hdf5 1.10.6 nompi_h6a2412b_1114 conda-forge icu 68.1 h58526e2_0 conda-forge idna 3.1 pyhd3deb0d_0 conda-forge importlib-metadata 4.8.1 py39hf3d152e_0 conda-forge importlib_metadata 4.8.1 hd8ed1ab_0 conda-forge importlib_resources 5.2.2 pyhd8ed1ab_0 conda-forge iprpy-data 2021.2.23 pyh44b312d_0 conda-forge ipykernel 6.4.1 py39hef51801_0 conda-forge ipython 7.27.0 py39hef51801_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.6.5 pyhd8ed1ab_0 conda-forge itsdangerous 2.0.1 pyhd8ed1ab_0 conda-forge jbig 2.1 h7f98852_2003 conda-forge jedi 0.18.0 py39hf3d152e_2 conda-forge jinja2 3.0.1 pyhd8ed1ab_0 conda-forge joblib 1.0.1 pyhd8ed1ab_0 conda-forge jpeg 9d h36c2ea0_0 conda-forge json5 0.9.5 pyh9f0ad1d_0 conda-forge jsoncpp 1.9.4 h4bd325d_3 conda-forge jsonschema 3.2.0 pyhd8ed1ab_3 conda-forge jupyter_client 7.0.3 pyhd8ed1ab_0 conda-forge jupyter_core 4.8.1 py39hf3d152e_0 conda-forge jupyter_server 1.11.0 pyhd8ed1ab_0 conda-forge jupyter_telemetry 0.1.0 pyhd8ed1ab_1 conda-forge jupyterhub 1.4.2 py39hf3d152e_0 conda-forge jupyterhub-base 1.4.2 py39hf3d152e_0 conda-forge jupyterlab 3.1.13 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge jupyterlab_server 2.8.2 pyhd8ed1ab_0 conda-forge jupyterlab_widgets 1.0.2 pyhd8ed1ab_0 conda-forge kim-api 2.2.1 h5c8ed42_0 conda-forge kiwisolver 1.3.2 py39h1a9c180_0 conda-forge krb5 1.19.2 hcc1bbae_1 conda-forge lame 3.100 h7f98852_1001 conda-forge lammps 2021.07.30 py39h910f28c_openmpi_1 conda-forge latexcodec 2.0.1 pyh9f0ad1d_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 libarchive 3.5.2 hccf745f_1 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 7.79.1 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 3.3 h58526e2_2 conda-forge libgcc-ng 11.2.0 h1d223b6_8 conda-forge libgfortran-ng 11.2.0 h69a702a_9 conda-forge libgfortran5 11.2.0 h5c6108e_9 conda-forge libglib 2.68.4 h3e27bee_0 conda-forge libglu 9.0.0 he1b5a44_1001 conda-forge libgomp 11.2.0 h1d223b6_8 conda-forge libiconv 1.16 h516909a_0 conda-forge libidn2 2.3.2 h7f98852_0 conda-forge liblapack 3.9.0 11_linux64_openblas conda-forge libllvm11 11.1.0 hf817b99_2 conda-forge libnetcdf 4.8.1 nompi_hcd642e3_100 conda-forge libnghttp2 1.43.0 h812cca2_1 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 libsodium 1.0.18 h36c2ea0_1 conda-forge libsolv 0.7.19 h780b84a_5 conda-forge libssh2 1.10.0 ha56f1ee_2 conda-forge libstdcxx-ng 11.2.0 he4da1e4_8 conda-forge libtheora 1.1.1 h7f98852_1005 conda-forge libtiff 4.3.0 hf544144_1 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libuv 1.41.1 h7f98852_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp-base 1.2.1 h7f98852_0 conda-forge libxc 4.3.4 h86c2bf4_2 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 libzip 1.8.0 h4de3113_1 conda-forge llvm-openmp 12.0.1 h4bd325d_1 conda-forge loguru 0.5.3 py39hf3d152e_2 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge lzo 2.10 h516909a_1000 conda-forge mako 1.1.5 pyhd8ed1ab_0 conda-forge mamba 0.15.3 py39h951de11_0 conda-forge markupsafe 2.0.1 py39h3811e60_0 conda-forge matplotlib-base 3.4.3 py39h2fa2bec_1 conda-forge matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge mendeleev 0.9.0 pyh8a188c0_0 conda-forge mistune 0.8.4 py39h3811e60_1004 conda-forge mkl 2020.4 h726a3e6_304 conda-forge mlip 1.0 hf1f3868_2 conda-forge mock 4.0.3 py39hf3d152e_1 conda-forge monty 2021.8.17 pyhd8ed1ab_0 conda-forge mpc 1.2.1 h9f54685_0 conda-forge mpfr 4.1.0 h9202a9a_1 conda-forge mpi 1.0 openmpi conda-forge mpmath 1.2.1 pyhd8ed1ab_0 conda-forge mysql-common 8.0.25 ha770c72_2 conda-forge mysql-libs 8.0.25 hfa10184_2 conda-forge n2p2 2.1.1 py39hccc7027_0 conda-forge nbclassic 0.3.2 pyhd8ed1ab_0 conda-forge nbclient 0.5.4 pyhd8ed1ab_0 conda-forge nbconvert 6.2.0 py39hf3d152e_0 conda-forge nbformat 5.1.3 pyhd8ed1ab_0 conda-forge ncurses 6.2 h58526e2_4 conda-forge nest-asyncio 1.5.1 pyhd8ed1ab_0 conda-forge netcdf4 1.5.7 nompi_py39hd2e3950_101 conda-forge nettle 3.6 he412f7d_0 conda-forge networkx 2.5 py_0 conda-forge nglview 3.0.3 pyh8a188c0_0 conda-forge nodejs 15.14.0 h92b4a50_0 conda-forge notebook 6.4.4 pyha770c72_0 conda-forge nspr 4.30 h9c3ff4c_0 conda-forge nss 3.69 hb5efdd6_1 conda-forge numexpr 2.7.3 py39hde0f152_0 conda-forge numpy 1.21.2 py39hdbf815f_0 conda-forge oauthlib 3.1.1 pyhd8ed1ab_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openh264 2.1.1 h780b84a_0 conda-forge openjpeg 2.4.0 hb52868f_1 conda-forge openkim-models 2021.01.28 h2cc385e_1 conda-forge openmpi 4.1.1 hbfc84c5_0 conda-forge openssl 1.1.1l h7f98852_0 conda-forge packaging 21.0 pyhd8ed1ab_0 conda-forge palettable 3.3.0 py_0 conda-forge pamela 1.0.0 py_0 conda-forge pandas 1.3.3 py39hde0f152_0 conda-forge pandoc 2.14.2 h7f98852_0 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge paramiko 2.7.2 pyh9f0ad1d_0 conda-forge parso 0.8.2 pyhd8ed1ab_0 conda-forge pathlib2 2.3.6 py39hf3d152e_0 conda-forge patsy 0.5.2 pyhd8ed1ab_0 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge pcre2 10.37 h032f7d1_0 conda-forge perl 5.32.1 0_h7f98852_perl5 conda-forge pexpect 4.8.0 pyh9f0ad1d_2 conda-forge phonopy 2.11.0 py39hce5d2b2_1 conda-forge pickleshare 0.7.5 py39hde42818_1002 conda-forge pillow 8.3.2 py39ha612740_0 conda-forge pint 0.17 pyhd8ed1ab_1 conda-forge pip 21.2.4 pyhd8ed1ab_0 conda-forge pkg-config 0.29.2 h36c2ea0_1008 conda-forge plotly 5.3.1 pyhd8ed1ab_0 conda-forge proj 8.1.0 h277dcde_1 conda-forge prometheus_client 0.11.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.20 pyha770c72_0 conda-forge psutil 5.8.0 py39h3811e60_1 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pugixml 1.11.4 h9c3ff4c_0 conda-forge pybtex 0.24.0 py39hf3d152e_0 conda-forge pycosat 0.6.3 py39h3811e60_1006 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pycurl 7.44.1 py39h72e3413_0 conda-forge pyfiglet 0.8.post1 py_0 conda-forge pyfileindex 0.0.6 pyhd8ed1ab_0 conda-forge pygments 2.10.0 pyhd8ed1ab_0 conda-forge pyiron 0.4.5 pyhd8ed1ab_0 conda-forge pyiron-data 0.0.16 hd8ed1ab_0 conda-forge pyiron_atomistics 0.2.26 pyhd8ed1ab_0 conda-forge pyiron_base 0.3.5 pyhd8ed1ab_0 conda-forge pyjwt 2.1.0 pyhd8ed1ab_0 conda-forge pymatgen 2022.0.14 py39h1a9c180_0 conda-forge pynacl 1.4.0 py39h3811e60_2 conda-forge pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyrsistent 0.17.3 py39h3811e60_2 conda-forge pyscal 2.10.14 py39h5472131_1 conda-forge pysocks 1.7.1 py39hf3d152e_3 conda-forge pysqa 0.0.15 pyhd8ed1ab_0 conda-forge pytables 3.6.1 py39hf6dc253_3 conda-forge python 3.9.6 h49503c6_1_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.1 pyh9f0ad1d_0 conda-forge python_abi 3.9 2_cp39 conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge pyyaml 5.4.1 py39h3811e60_1 conda-forge pyzmq 22.3.0 py39h37b5a0c_0 conda-forge qt 5.12.9 hda022c4_4 conda-forge quippy 0.0.1 py39hbb6cefa_2 conda-forge readline 8.1 h46c0cb4_0 conda-forge reproc 14.2.3 h7f98852_0 conda-forge reproc-cpp 14.2.3 h9c3ff4c_0 conda-forge requests 2.26.0 pyhd8ed1ab_0 conda-forge requests-unixsocket 0.2.0 py_0 conda-forge ruamel.yaml 0.17.16 py39h3811e60_0 conda-forge ruamel.yaml.clib 0.2.2 py39h3811e60_2 conda-forge ruamel_yaml 0.15.80 py39h3811e60_1004 conda-forge scalapack 2.0.2 hc7fdd6d_1009 conda-forge scandir 1.10.0 py39h3811e60_3 conda-forge scikit-learn 1.0 py39h7c5d8c9_1 conda-forge scipy 1.7.1 py39hee8e79c_0 conda-forge seaborn 0.11.2 hd8ed1ab_0 conda-forge seaborn-base 0.11.2 pyhd8ed1ab_0 conda-forge seekpath 2.0.1 pyh44b312d_1 conda-forge send2trash 1.8.0 pyhd8ed1ab_0 conda-forge setuptools 58.0.4 py39hf3d152e_2 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge smmap 3.0.5 pyh44b312d_0 conda-forge sniffio 1.2.0 py39hf3d152e_1 conda-forge spglib 1.16.2 py39hce5d2b2_0 conda-forge sphinxdft 3.0.3 h7f852f6_1 conda-forge sphinxdft-data 0.0.1 hd8ed1ab_2 conda-forge sqlalchemy 1.4.25 py39h3811e60_0 conda-forge sqlite 3.36.0 h9cd32fc_2 conda-forge statsmodels 0.12.2 py39hce5d2b2_0 conda-forge sympy 1.8 py39hf3d152e_0 conda-forge tabulate 0.8.9 pyhd8ed1ab_0 conda-forge tbb 2020.2 h4bd325d_4 conda-forge tbb-devel 2020.2 h4bd325d_4 conda-forge tenacity 8.0.1 pyhd8ed1ab_0 conda-forge terminado 0.12.1 py39hf3d152e_0 conda-forge testpath 0.5.0 pyhd8ed1ab_0 conda-forge threadpoolctl 2.2.0 pyh8a188c0_0 conda-forge tk 8.6.11 h27826a3_1 conda-forge tornado 6.1 py39h3811e60_1 conda-forge tqdm 4.62.3 pyhd8ed1ab_0 conda-forge traitlets 5.1.0 pyhd8ed1ab_0 conda-forge typing_extensions 3.10.0.2 pyha770c72_0 conda-forge tzdata 2021a he74cb21_1 conda-forge uncertainties 3.1.6 pyhd8ed1ab_0 conda-forge urllib3 1.26.7 pyhd8ed1ab_0 conda-forge utfcpp 3.2.1 ha770c72_0 conda-forge vtk 9.0.3 no_osmesa_py39hb68e339_103 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge websocket-client 0.57.0 py39hf3d152e_4 conda-forge werkzeug 2.0.1 pyhd8ed1ab_0 conda-forge wget 1.20.3 ha56f1ee_1 conda-forge wheel 0.37.0 pyhd8ed1ab_1 conda-forge widgetsnbextension 3.5.1 py39hf3d152e_4 conda-forge x264 1!161.3030 h7f98852_1 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.7.2 h7f98852_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h7f98852_1 conda-forge xorg-libxt 1.2.1 h7f98852_2 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h516909a_0 conda-forge zeromq 4.3.4 h9c3ff4c_1 conda-forge zipp 3.5.0 pyhd8ed1ab_0 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstd 1.5.0 ha95c52a_0 conda-forge

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max-hassani commented 2 years ago

From the first look, in the CI workflow, the list of the installed packages does not include mkl or openmpi packages. I guess they are installed by the based docker container which runs the workflow. I compare it with the details in the log: https://github.com/pyiron/pyiron_atomistics/runs/3734658434 Without the complete info of the CI, it is hard to say the difference between the two. I can create a test PR and print out the whole conda environment.

jan-janssen commented 2 years ago

You can add conda list to the continuous integration by adding the corresponding line to the tests for the jupyter notebooks, like I did in https://github.com/pyiron/pyiron_atomistics/pull/383

jan-janssen commented 2 years ago 
Run conda list
# packages in environment at/usr/share/miniconda/envs/test:
# Name                    Version                   Build Channel
_libgcc_mutex             0.1                 conda_orge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
aimsgb                    0.1.0              pyhd8ed1ab_1    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
ansiwrap                  0.8.4                      py_0    conda-forge
argon2-cffi               20.1.0           py39h3811e60_2    conda-forge
ase                       3.22.0             pyhd8ed1ab_0    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     21.2.0             pyhd8ed1ab_0    conda-forge
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
bcrypt                    3.2.0            py39h3811e60_1    conda-forge
black                     21.9b0             pyhd8ed1ab_0    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.0               h9c3ff4c_0    conda-forge
brotlipy                  0.7.0           py39h3811e60_1001    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
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2021.5.30        py39hf3d152e_0    conda-forge
cffi                      1.14.6           py39h4bc2ebd_1    conda-forge
cftime                    1.5.1            py39hce5d2b2_0    conda-forge
chardet                   4.0.0            py39hf3d152e_1    conda-forge
charset-normalizer        2.0.0              pyhd8ed1ab_0    conda-forge
click                     8.0.1            py39hf3d152e_0    conda-forge
codacy-coverage           1.3.11             pyhd8ed1ab_1    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
coverage                  5.5              py39h3811e60_0    conda-forge
coveralls                 3.2.0              pyhd8ed1ab_0    conda-forge
cryptography              3.4.7            py39hbca0aa6_0    conda-forge
curl                      7.79.1               h2574ce0_1    conda-forge
cycler                    0.10.0                     py_2    conda-forge
cython                    0.29.24          py39he80948d_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
dbus                      1.13.6               h48d8840_2    conda-forge
debugpy                   1.4.1            py39he80948d_0    conda-forge
decorator                 5.1.0              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dill                      0.3.4              pyhd8ed1ab_0    conda-forge
docopt                    0.6.2                      py_1    conda-forge
double-conversion         3.1.5                h9c3ff4c_2    conda-forge
eigen                     3.4.0                h4bd325d_0    conda-forge
entrypoints               0.3             py39hde42818_1002    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
f90wrap                   0.2.7            py39h984b4d8_0    conda-forge
ffmpeg                    4.3.2                hca11adc_0    conda-forge
fftw                      3.3.10          nompi_h74d3f13_101    conda-forge
flask                     2.0.1              pyhd8ed1ab_0    conda-forge
fontconfig                2.13.1            hba837de_1005    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
future                    0.18.2           py39hf3d152e_3    conda-forge
gettext                   0.19.8.1          h73d1719_1008    conda-forge
git                       2.33.0          pl5321hc30692c_1    conda-forge
gitdb                     4.0.7              pyhd8ed1ab_0    conda-forge
gitpython                 3.1.24             pyhd8ed1ab_0    conda-forge
gl2ps                     1.4.2                h0708190_0    conda-forge
glew                      2.1.0                h9c3ff4c_2    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
gnutls                    3.6.13               h85f3911_1    conda-forge
gpaw                      21.6.0           py39_openmpi_1    conda-forge
gpaw-data                 0.9.20000                     0    conda-forge
greenlet                  1.1.2            py39he80948d_0    conda-forge
gsl                       2.6                  he838d99_2    conda-forge
gst-plugins-base          1.18.5               hf529b03_0    conda-forge
gstreamer                 1.18.5               h76c114f_0    conda-forge
h5io                      0.1.2              pyh95af2a2_0    conda-forge
h5py                      3.3.0           nompi_py39h98ba4bc_100    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.10.6          nompi_h6a2412b_1114    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
idna                      3.1                pyhd3deb0d_0    conda-forge
importlib-metadata        4.8.1            py39hf3d152e_0    conda-forge
importlib_metadata        4.8.1                hd8ed1ab_0    conda-forge
importlib_resources       5.2.2              pyhd8ed1ab_0    conda-forge
intel-openmp              2021.3.0          h06a4308_3350  
iprpy-data                2021.2.23          pyh44b312d_0    conda-forge
ipykernel                 6.4.1            py39hef51801_0    conda-forge
ipython                   7.28.0           py39hef51801_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.5              pyhd8ed1ab_0    conda-forge
itsdangerous              2.0.1              pyhd8ed1ab_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.0           py39hf3d152e_2    conda-forge
jinja2                    3.0.1              pyhd8ed1ab_0    conda-forge
joblib                    1.0.1              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
jsoncpp                   1.9.4                h4bd325d_3    conda-forge
jsonschema                4.0.1              pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0            py39hf3d152e_6    conda-forge
jupyter_client            7.0.5              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.0              pyhd8ed1ab_0    conda-forge
jupyter_core              4.8.1            py39hf3d152e_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_widgets        1.0.2              pyhd8ed1ab_0    conda-forge
kim-api                   2.2.1                h5c8ed42_0    conda-forge
kiwisolver                1.3.2            py39h1a9c180_0    conda-forge
krb5                      1.19.2               hcc1bbae_2    conda-forge
lame                      3.100             h7f98852_1001    conda-forge
lammps                    2021.07.30      py39h910f28c_openmpi_1    conda-forge
latexcodec                2.0.1              pyh9f0ad1d_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                   7.79.1               h2574ce0_1    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_4    conda-forge
libgcc-ng                 11.2.0               h1d223b6_9    conda-forge
libgfortran-ng            11.2.0               h69a702a_9    conda-forge
libgfortran5              11.2.0               h5c6108e_9    conda-forge
libglib                   2.68.4               h174f98d_1    conda-forge
libglu                    9.0.0             he1b5a44_1001    conda-forge
libgomp                   11.2.0               h1d223b6_9    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libidn2                   2.3.2                h7f98852_0    conda-forge
liblapack                 3.9.0           11_linux64_openblas    conda-forge
libllvm11                 11.1.0               hf817b99_2    conda-forge
libnetcdf                 4.8.1           nompi_hcd642e3_100    conda-forge
libnghttp2                1.43.0               h812cca2_1    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
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              11.2.0               he4da1e4_9    conda-forge
libtheora                 1.1.1             h7f98852_1005    conda-forge
libtiff                   4.3.0                hf544144_1    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.2.1                h7f98852_0    conda-forge
libxc                     4.3.4                h86c2bf4_2    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
libzip                    1.8.0                h4de3113_1    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
loguru                    0.5.3            py39hf3d152e_2    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markupsafe                2.0.1            py39h3811e60_0    conda-forge
matplotlib-base           3.4.3            py39h2fa2bec_1    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mendeleev                 0.9.0              pyh8a188c0_0    conda-forge
mistune                   0.8.4           py39h3811e60_1004    conda-forge
mkl                       2021.3.0           h06a4308_520  
mlip                      1.0                  hf1f3868_2    conda-forge
mock                      4.0.3            py39hf3d152e_1    conda-forge
monty                     2021.8.17          pyhd8ed1ab_0    conda-forge
mpc                       1.2.1                h9f54685_0    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
mpi                       1.0                     openmpi    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
mypy_extensions           0.4.3            py39hf3d152e_3    conda-forge
mysql-common              8.0.25               ha770c72_2    conda-forge
mysql-libs                8.0.25               hfa10184_2    conda-forge
n2p2                      2.1.1            py39hccc7027_0    conda-forge
nbclient                  0.5.4              pyhd8ed1ab_0    conda-forge
nbconvert                 6.2.0            py39hf3d152e_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
netcdf4                   1.5.7           nompi_py39hd2e3950_101    conda-forge
nettle                    3.6                  he412f7d_0    conda-forge
networkx                  2.5                        py_0    conda-forge
nglview                   3.0.3              pyh8a188c0_0    conda-forge
notebook                  6.4.4              pyha770c72_0    conda-forge
nspr                      4.30                 h9c3ff4c_0    conda-forge
nss                       3.69                 hb5efdd6_1    conda-forge
numexpr                   2.7.3            py39hde0f152_0    conda-forge
numpy                     1.21.2           py39hdbf815f_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openh264                  2.1.1                h780b84a_0    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openmpi                   4.1.1                hbfc84c5_0    conda-forge
openssl                   1.1.1l               h7f98852_0    conda-forge
packaging                 21.0               pyhd8ed1ab_0    conda-forge
palettable                3.3.0                      py_0    conda-forge
pandas                    1.3.3            py39hde0f152_0    conda-forge
pandoc                    2.14.2               h7f98852_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
papermill                 2.3.3              pyhd8ed1ab_0    conda-forge
paramiko                  2.7.2              pyh9f0ad1d_0    conda-forge
parso                     0.8.2              pyhd8ed1ab_0    conda-forge
pathlib2                  2.3.6            py39hf3d152e_0    conda-forge
pathspec                  0.9.0              pyhd8ed1ab_0    conda-forge
patsy                     0.5.2              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.37                h032f7d1_0    conda-forge
perl                      5.32.1          0_h7f98852_perl5    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
phonopy                   2.11.0           py39hce5d2b2_1    conda-forge
pickleshare               0.7.5           py39hde42818_1002    conda-forge
pillow                    8.3.2            py39ha612740_0    conda-forge
pint                      0.17               pyhd8ed1ab_1    conda-forge
pip                       21.2.4             pyhd8ed1ab_0    conda-forge
pkg-config                0.29.2            h36c2ea0_1008    conda-forge
platformdirs              2.3.0              pyhd8ed1ab_0    conda-forge
plotly                    5.3.1              pyhd8ed1ab_0    conda-forge
proj                      8.1.1                h277dcde_2    conda-forge
prometheus_client         0.11.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.20             pyha770c72_0    conda-forge
prompt_toolkit            3.0.20               hd8ed1ab_0    conda-forge
psutil                    5.8.0            py39h3811e60_1    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pugixml                   1.11.4               h9c3ff4c_0    conda-forge
pybtex                    0.24.0           py39hf3d152e_0    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pyfiglet                  0.8.post1                  py_0    conda-forge
pyfileindex               0.0.6              pyhd8ed1ab_0    conda-forge
pygments                  2.10.0             pyhd8ed1ab_0    conda-forge
pyiron-data               0.0.16               hd8ed1ab_0    conda-forge
pyiron_base               0.3.5              pyhd8ed1ab_0    conda-forge
pymatgen                  2022.0.14        py39h1a9c180_0    conda-forge
pynacl                    1.4.0            py39h3811e60_2    conda-forge
pyopenssl                 21.0.0             pyhd8ed1ab_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
pyrsistent                0.17.3           py39h3811e60_2    conda-forge
pyscal                    2.10.12          py39h5472131_0    conda-forge
pysocks                   1.7.1            py39hf3d152e_3    conda-forge
pysqa                     0.0.15             pyhd8ed1ab_0    conda-forge
pytables                  3.6.1            py39hf6dc253_3    conda-forge
python                    3.9.7           hb7a2778_3_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytz                      2021.1             pyhd8ed1ab_0    conda-forge
pyyaml                    5.4.1            py39h3811e60_1    conda-forge
pyzmq                     22.3.0           py39h37b5a0c_0    conda-forge
qt                        5.12.9               hda022c4_4    conda-forge
qtconsole                 5.1.1              pyhd8ed1ab_0    conda-forge
qtpy                      1.11.2             pyhd8ed1ab_0    conda-forge
quippy                    0.0.1            py39hbb6cefa_2    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
regex                     2021.9.30        py39h3811e60_0    conda-forge
requests                  2.26.0             pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.17.16          py39h3811e60_0    conda-forge
ruamel.yaml.clib          0.2.2            py39h3811e60_2    conda-forge
scalapack                 2.0.2             hc7fdd6d_1009    conda-forge
scandir                   1.10.0           py39h3811e60_3    conda-forge
scikit-learn              1.0              py39h7c5d8c9_1    conda-forge
scipy                     1.7.1            py39hee8e79c_0    conda-forge
seaborn                   0.11.2               hd8ed1ab_0    conda-forge
seaborn-base              0.11.2             pyhd8ed1ab_0    conda-forge
seekpath                  2.0.1              pyh44b312d_1    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                58.0.4           py39hf3d152e_2    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
spglib                    1.16.2           py39hce5d2b2_0    conda-forge
sphinxdft                 3.0.3                h7f852f6_1    conda-forge
sphinxdft-data            0.0.1                hd8ed1ab_2    conda-forge
sqlalchemy                1.4.25           py39h3811e60_0    conda-forge
sqlite                    3.36.0               h9cd32fc_2    conda-forge
sqsgenerator              0.0.5            py39h81fec48_2    conda-forge
statsmodels               0.13.0           py39hce5d2b2_0    conda-forge
sympy                     1.8              py39hf3d152e_0    conda-forge
tabulate                  0.8.9              pyhd8ed1ab_0    conda-forge
tbb                       2020.2               h4bd325d_4    conda-forge
tbb-devel                 2020.2               h4bd325d_4    conda-forge
tenacity                  8.0.1              pyhd8ed1ab_0    conda-forge
terminado                 0.12.1           py39hf3d152e_0    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
textwrap3                 0.9.2                      py_0    conda-forge
threadpoolctl             3.0.0              pyh8a188c0_0    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
tomli                     1.2.1              pyhd8ed1ab_0    conda-forge
tornado                   6.1              py39h3811e60_1    conda-forge
tqdm                      4.62.3             pyhd8ed1ab_0    conda-forge
traitlets                 5.1.0              pyhd8ed1ab_0    conda-forge
typed-ast                 1.4.3            py39h3811e60_0    conda-forge
typing_extensions         3.10.0.2           pyha770c72_0    conda-forge
tzdata                    2021b                he74cb21_0    conda-forge
uncertainties             3.1.6              pyhd8ed1ab_0    conda-forge
urllib3                   1.26.7             pyhd8ed1ab_0    conda-forge
utfcpp                    3.2.1                ha770c72_0    conda-forge
vtk                       9.0.3           no_osmesa_py39h1bd5e71_104    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
werkzeug                  2.0.1              pyhd8ed1ab_0    conda-forge
wget                      1.20.3               ha56f1ee_1    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        3.5.1            py39hf3d152e_4    conda-forge
x264                      1!161.3030           h7f98852_1    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h516909a_0    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.6.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge
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jan-janssen commented 2 years ago

@muh-hassani Can you try mkl=2021.3.0 ? Once this is working we should fix the version number for the conda package.

max-hassani commented 2 years ago

@jan-janssen, thanks for the PR. There seems to be a conflict between pyiron_atomistic dependencies and mkl=2021.3.0; when I removed pyiron_atomistics version, pyiron_atomistics=0.2.3 got installed!
Tomorrow, I will take a closer look at the list of dependencies, to find out the issue.

jan-janssen commented 2 years ago

I fixed the Sphinx issue - https://github.com/pyiron/docker-stacks/pull/95 - but there is still an issue with the experimental notebooks and we are still using the outdated Damask version, so this should also be updated. In addition I opened a pull request to bind the mkl version: https://github.com/conda-forge/sphinxdft-feedstock/pull/32 . Finally I noticed that we are not using the latest version of LAMMPS so there seem to be some outdated packages in out dependencies.