MoleculeKit: Logging setup failed + Could not find moleculekit share directory.

[Hyeri-Lim]

Dear acellera group,

For the last one weeks, I have been trying to use htmd and met the following error.

MoleculeKit: Logging setup failed 'Could not find moleculekit share directory.'

I operate htmd with python 3.9.13　htmd 2.2. conda version: conda 22.9.0 via linux system

actually I tried to install htmd with command "conda install htmd=2.2.0 python=3.10 -c acellera -c conda-forge" (https://github.com/Acellera/htmd/issues/1038#issuecomment-1283528192) because there was [glibc_2.29 not found error] issues. but after that, also MoleculeKit issue was happened that I downgraded python version 3.9 and put the command below.

conda install moleculekit python=3.9 -c acellera -c conda-forge

but still [MoleculeKit: Logging setup failed] is happened. Do you know how to solve it? Thank you in advance.

also here is my whole conda list.

Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
acemd3                    3.5.1                cuda1121_0    acellera
alsa-lib                  1.2.7.2              h166bdaf_0    conda-forge
amberlite                 22.0                     pypi_0    pypi
ambertools                22.0             py39hcb9d944_3    conda-forge
amberutils                21.0                     pypi_0    pypi
anaconda-client           1.8.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39hb9d737c_2    conda-forge
arpack                    3.7.0                hdefa2d7_2    conda-forge
asttokens                 2.0.8              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
attr                      2.5.1                h166bdaf_1    conda-forge
attrs                     22.1.0             pyh71513ae_1    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
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
biopython                 1.79             py39hb9d737c_2    conda-forge
bleach                    5.0.1              pyhd8ed1ab_0    conda-forge
blosc                     1.21.1               h83bc5f7_3    conda-forge
boost                     1.74.0           py39h5472131_5    conda-forge
boost-cpp                 1.74.0               h75c5d50_8    conda-forge
brotli                    1.0.9                h166bdaf_7    conda-forge
brotli-bin                1.0.9                h166bdaf_7    conda-forge
brotlipy                  0.7.0           py39hb9d737c_1004    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.07.19           h06a4308_0  
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.16.0            ha61ee94_1014    conda-forge
certifi                   2022.9.24        py39h06a4308_0  
cffi                      1.15.1           py39he91dace_1    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
clyent                    1.2.2                      py_1    conda-forge
colorama                  0.4.5              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.5            py39hf939315_0    conda-forge
cryptography              38.0.2           py39hd97740a_0    conda-forge
cudatoolkit               11.2.2              hbe64b41_10    conda-forge
curl                      7.85.0               h7bff187_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.32          py39h5a03fae_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
debugpy                   1.6.3            py39h5a03fae_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
deeptime                  0.4.3            py39h1832856_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dill                      0.3.5.1            pyhd8ed1ab_0    conda-forge
docutils                  0.16             py39hf3d152e_3    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
et_xmlfile                1.0.1                   py_1001    conda-forge
executing                 1.1.1              pyhd8ed1ab_0    conda-forge
expat                     2.4.9                h27087fc_0    conda-forge
ffevaluation              0.1.9                    py39_0    acellera
fftw                      3.3.10          nompi_hf0379b8_105    conda-forge
fire                      0.4.0              pyh44b312d_0    conda-forge
flit-core                 3.7.1              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.0               hc2a2eb6_1    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.37.4           py39hb9d737c_0    conda-forge
freetype                  2.12.1               hca18f0e_0    conda-forge
gawk                      5.1.0                h7f98852_0    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
glew                      2.1.0                h9c3ff4c_2    conda-forge
glib                      2.74.0               h6239696_0    conda-forge
glib-tools                2.74.0               h6239696_0    conda-forge
glm                       0.9.9.4              h924138e_2    conda-forge
greenlet                  1.1.3            py39h5a03fae_0    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gst-plugins-base          1.20.3               h57caac4_2    conda-forge
gstreamer                 1.20.3               hd4edc92_2    conda-forge
h5py                      3.7.0           nompi_py39hd51670d_101    conda-forge
hdf4                      4.2.15               h9772cbc_4    conda-forge
hdf5                      1.12.2          nompi_h2386368_100    conda-forge
htmd                      2.2.0                    py39_0    acellera
htmd-deps                 2.2.0                    py39_0    acellera
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.4           py39hf3d152e_0    conda-forge
importlib_resources       5.10.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.16.0             pyh210e3f2_0    conda-forge
ipython                   8.5.0              pyh41d4057_1    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.5              pyhd8ed1ab_0    conda-forge
jack                      1.9.18            h8c3723f_1003    conda-forge
jedi                      0.18.1             pyhd8ed1ab_2    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.2.0              pyhd8ed1ab_0    conda-forge
jobqueues                 0.8.3                    py39_0    acellera
jpeg                      9e                   h166bdaf_2    conda-forge
jsonschema                4.16.0             pyhd8ed1ab_0    conda-forge
jupyter_client            7.4.2              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.4              pyhd8ed1ab_0    conda-forge
jupyter_core              4.11.1           py39hf3d152e_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.3              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4            py39hf939315_0    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.38                 h1181459_1  
lerc                      4.0.0                h27087fc_0    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_7    conda-forge
libbrotlidec              1.0.9                h166bdaf_7    conda-forge
libbrotlienc              1.0.9                h166bdaf_7    conda-forge
libcap                    2.65                 ha37c62d_0    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libclang                  14.0.6          default_hc1a23ef_0  
libclang13                14.0.6          default_h31cde19_0  
libcups                   2.3.3                h3e49a29_2    conda-forge
libcurl                   7.85.0               h7bff187_0    conda-forge
libdb                     6.2.32               h9c3ff4c_0    conda-forge
libdeflate                1.14                 h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.3.4                h27087fc_0    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
libglib                   2.74.0               h7a41b64_0    conda-forge
libglu                    9.0.0             he1b5a44_1001    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libllvm11                 11.1.0               he0ac6c6_4    conda-forge
libllvm14                 14.0.6               he0ac6c6_0    conda-forge
libnetcdf                 4.8.1           nompi_h21705cb_104    conda-forge
libnghttp2                1.47.0               hdcd2b5c_1    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.38               h753d276_0    conda-forge
libpq                     14.5                 hd77ab85_0    conda-forge
libsndfile                1.0.31               h9c3ff4c_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.39.4               h753d276_0    conda-forge
libssh2                   1.10.0               haa6b8db_3    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libtiff                   4.4.0                h55922b4_4    conda-forge
libtool                   2.4.6             h9c3ff4c_1008    conda-forge
libudev1                  249                  h166bdaf_4    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.2.4                h166bdaf_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.10.2               h7463322_2    conda-forge
libzip                    1.9.2                hc869a4a_1    conda-forge
libzlib                   1.2.12               h166bdaf_3    conda-forge
llvmlite                  0.39.1           py39h7d9a04d_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markupsafe                2.1.1            py39hb9d737c_1    conda-forge
matplotlib                3.6.1            py39hf3d152e_0    conda-forge
matplotlib-base           3.6.1            py39hf9fd14e_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mdtraj                    1.9.7            py39hc79b4f4_2    conda-forge
mistune                   2.0.4              pyhd8ed1ab_0    conda-forge
mmcif_pdbx                2.0.0              pyh44b312d_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
mmtf-python               1.1.3              pyhd8ed1ab_0    conda-forge
moleculekit               1.4.9                    py39_0    acellera
msgpack-python            1.0.4            py39hf939315_0    conda-forge
multiprocess              0.70.13          py39hb9d737c_1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              8.0.31               haf5c9bc_0    conda-forge
mysql-libs                8.0.31               h28c427c_0    conda-forge
natsort                   8.2.0              pyhd8ed1ab_0    conda-forge
nbclient                  0.7.0              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.1              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.1              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.1              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h5eee18b_3  
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.0           nompi_hc402ea5_101    conda-forge
networkx                  2.8.7              pyhd8ed1ab_0    conda-forge
nglview                   3.0.3              pyh8a188c0_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
notebook                  6.4.12             pyha770c72_0    conda-forge
nspr                      4.32                 h9c3ff4c_1    conda-forge
nss                       3.78                 h2350873_0    conda-forge
numba                     0.56.3           py39h61ddf18_0    conda-forge
numexpr                   2.8.3           py39h194a79d_100    conda-forge
numpy                     1.23.4           py39h3d75532_0    conda-forge
ocl-icd                   2.3.1                h7f98852_0    conda-forge
ocl-icd-system            1.0.0                         1    conda-forge
openbabel                 3.1.1            py39h71cce9b_4    conda-forge
openjpeg                  2.5.0                h7d73246_1    conda-forge
openmm                    7.7.0            py39h15fbce5_1    conda-forge
openpyxl                  3.0.10           py39hb9d737c_1    conda-forge
openssl                   1.1.1q               h7f8727e_0  
packaging                 21.3               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h86c2bf4_0    conda-forge
packmol-memgen            1.2.3rc0                 pypi_0    pypi
pandas                    1.5.1            py39h4661b88_0    conda-forge
pandoc                    2.19.2               ha770c72_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parmed                    3.4.3            py39h5a03fae_2    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pathos                    0.2.9              pyhd8ed1ab_0    conda-forge
pcre2                     10.37                hc3806b6_1    conda-forge
pdb2pqr                   3.5.2+20                   py_0    acellera
pdb4amber                 22.0                     pypi_0    pypi
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.2.0            py39hd5dbb17_2    conda-forge
pint                      0.19.2             pyhd8ed1ab_0    conda-forge
pip                       22.3               pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
plumed                    2.7.3           nompi_h8de8e23_100    conda-forge
plumed2                   2.3.3+htmd.4                  4    acellera
ply                       3.11                       py_1    conda-forge
pmw                       2.0.1           py39hf3d152e_1006    conda-forge
portaudio                 19.6.0               h8e90077_6    conda-forge
pox                       0.3.1              pyhd8ed1ab_0    conda-forge
ppft                      1.7.6.5            pyhd8ed1ab_0    conda-forge
prometheus_client         0.14.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.31             pyha770c72_0    conda-forge
prompt_toolkit            3.0.31               hd8ed1ab_0    conda-forge
propka                    3.4.0            py39hef51801_3    conda-forge
protocolinterface         0.4.5                      py_0    acellera
psfgen                    1.6.9                         0    acellera
psutil                    5.9.3            py39hb9d737c_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulseaudio                14.0                 h0868958_9    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycairo                   1.21.0           py39h0934665_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyemma                    2.5.12           py39h1832856_0    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pymol-open-source         2.5.0            py39hc95a48e_6    conda-forge
pyopenssl                 22.1.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.7           py39h18e9c17_1    conda-forge
pyqt5-sip                 12.11.0          py39h5a03fae_1    conda-forge
pyrsistent                0.18.1           py39hb9d737c_1    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.7.0            py39hee6f8ba_2    conda-forge
python                    3.9.13          h9a8a25e_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2022.4             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py39hb9d737c_4    conda-forge
pyzmq                     24.0.1           py39headdf64_0    conda-forge
qt-main                   5.15.6               hc525480_0    conda-forge
rdkit                     2022.03.5        py39h89e00b9_0    conda-forge
readline                  8.1.2                h7f8727e_1  
reportlab                 3.5.68           py39he59360d_1    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
sander                    22.0                     pypi_0    pypi
scikit-learn              1.1.2            py39he5e8d7e_0    conda-forge
scipy                     1.9.2            py39hddc5342_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                65.5.0             pyhd8ed1ab_0    conda-forge
sip                       6.7.2            py39h5a03fae_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.9                hbd366e4_1    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sqlalchemy                1.4.42           py39hb9d737c_0    conda-forge
sqlite                    3.39.3               h5082296_0  
stack_data                0.5.1              pyhd8ed1ab_0    conda-forge
termcolor                 2.0.1              pyhd8ed1ab_1    conda-forge
terminado                 0.16.0             pyh41d4057_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tinycss2                  1.1.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h1ccaba5_0  
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tornado                   6.2              py39hb9d737c_0    conda-forge
tqdm                      4.64.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.4.0              pyhd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022c                h04d1e81_0  
unicodedata2              14.0.0           py39hb9d737c_1    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
vina                      1.1.101                       0    acellera
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.37.1             pyhd3eb1b0_0  
widgetsnbextension        3.5.2            py39h06a4308_0  
xcb-util                  0.4.0                h166bdaf_0    conda-forge
xcb-util-image            0.4.0                h166bdaf_0    conda-forge
xcb-util-keysyms          0.4.0                h166bdaf_0    conda-forge
xcb-util-renderutil       0.3.9                h166bdaf_0    conda-forge
xcb-util-wm               0.4.1                h166bdaf_0    conda-forge
xdrfile                   1.1.4                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-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h5eee18b_0  
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.9.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.12               h5eee18b_3  
zstd                      1.5.2                h6239696_4    conda-forge

[stefdoerr]

I apologize for all these issues (it's usually not that bad). I tried this week to modernize the packaging and distribution of moleculekit and I've made a few mistakes on the way.

Please reinstall the latest moleculekit inside that env with: conda install moleculekit=1.5.0 -c acellera -c conda-forge This should fix it and I hope we don't hit any more issues going onward.

Best, Stefan