microsoft / molskill

Extracting medicinal chemistry intuition via preference machine learning
MIT License
104 stars 9 forks source link

Conda installer default NumPy version (2.0.1) incompatible with Molskill models #15

Closed vincenzo-palmacci closed 3 months ago

vincenzo-palmacci commented 3 months ago

I found that using the conda installer as suggested in the README installs a NumPy version that is incompatible with the models (np.Inf is not read correctly anymore). Hence I had to downgrade to NumPy 1.23.1 to make the code work.

Is there a possibility to solve this problem at the source and make the conda installer install the correct dependencies?

josejimenezluna commented 3 months ago

Hi @vincenzo-palmacci. I seem unable to reproduce this problem - on a freshly-created py310 environment the current installation procedure pulls numpy==1.26 instead of 2.0. We also do not use np.Inf (or np.inf for that matter) anywhere that I can see on the codebase.

Can you provide more details on how you were setting your environment?

(base) jjimenezluna@xxx:~$ mamba create -n mtest2 python=3.10 pip requests

Looking for: ['python=3.10', 'pip', 'requests']

pytorch/linux-64                                            Using cache
pytorch/noarch                                              Using cache
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
pkgs/main/linux-64                                            No change
pkgs/r/linux-64                                               No change
pkgs/r/noarch                                                 No change
pkgs/main/noarch                                              No change
Transaction                                                                                                                
  Prefix: /home/jjimenezluna/miniconda3/envs/mtest2

  Updating specs:

   - python=3.10
   - pip
   - requests

  Package                Version  Build            Channel        Size
────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────

  + ld_impl_linux-64        2.38  h1181459_1       pkgs/main     669kB
  + ca-certificates     2024.7.2  h06a4308_0       pkgs/main     130kB
  + _libgcc_mutex            0.1  main             pkgs/main       3kB
  + libstdcxx-ng          11.2.0  h1234567_1       pkgs/main       5MB
  + libgomp               11.2.0  h1234567_1       pkgs/main     485kB
  + _openmp_mutex            5.1  1_gnu            pkgs/main      21kB
  + libgcc-ng             11.2.0  h1234567_1       pkgs/main       6MB
  + xz                     5.4.6  h5eee18b_1       pkgs/main     659kB
  + openssl               3.0.14  h5eee18b_0       pkgs/main       5MB
  + libffi                 3.4.4  h6a678d5_1       pkgs/main     145kB
  + bzip2                  1.0.8  h5eee18b_6       pkgs/main     268kB
  + zlib                  1.2.13  h5eee18b_1       pkgs/main     113kB
  + ncurses                  6.4  h6a678d5_0       pkgs/main     936kB
  + libuuid               1.41.5  h5eee18b_0       pkgs/main      28kB
  + tk                    8.6.14  h39e8969_0       pkgs/main       4MB
  + readline                 8.2  h5eee18b_0       pkgs/main     365kB
  + sqlite                3.45.3  h5eee18b_0       pkgs/main       1MB
  + tzdata                 2024a  h04d1e81_0       pkgs/main     119kB
  + python               3.10.14  h955ad1f_1       pkgs/main      28MB
  + wheel                 0.43.0  py310h06a4308_0  pkgs/main     113kB
  + setuptools            72.1.0  py310h06a4308_0  pkgs/main       3MB
  + pip                     24.0  py310h06a4308_0  pkgs/main       3MB
  + pysocks                1.7.1  py310h06a4308_0  pkgs/main      29kB
  + brotli-python          1.0.9  py310h6a678d5_8  pkgs/main     365kB
  + idna                     3.7  py310h06a4308_0  pkgs/main     133kB
  + certifi             2024.7.4  py310h06a4308_0  pkgs/main     162kB
  + urllib3                2.2.2  py310h06a4308_0  pkgs/main     183kB
  + charset-normalizer     3.3.2  pyhd3eb1b0_0     pkgs/main      46kB
  + requests              2.32.3  py310h06a4308_0  pkgs/main     102kB

  Summary:

  Install: 29 packages

  Total download: 59MB

────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] Y
ld_impl_linux-64                                   669.2kB @   4.1MB/s  0.2s
_libgcc_mutex                                        3.5kB @  20.6kB/s  0.2s
libgomp                                            485.1kB @   2.5MB/s  0.2s
bzip2                                              268.4kB @   1.3MB/s  0.0s
libstdcxx-ng                                         4.9MB @  20.5MB/s  0.2s
ca-certificates                                    129.5kB @ 519.7kB/s  0.2s
wheel                                              112.6kB @ 435.2kB/s  0.1s
sqlite                                               1.3MB @   4.8MB/s  0.1s
pysocks                                             28.9kB @ 104.0kB/s  0.0s
requests                                           102.0kB @ 338.5kB/s  0.0s
certifi                                            162.2kB @ 527.2kB/s  0.1s
zlib                                               113.5kB @ 361.3kB/s  0.0s
xz                                                 658.9kB @   2.0MB/s  0.1s
idna                                               132.6kB @ 366.0kB/s  0.0s
readline                                           365.2kB @ 998.0kB/s  0.1s
_openmp_mutex                                       21.3kB @  56.6kB/s  0.0s
setuptools                                           2.5MB @   6.3MB/s  0.1s
libffi                                             144.7kB @ 355.2kB/s  0.0s
tzdata                                             119.1kB @ 292.3kB/s  0.0s
brotli-python                                      364.9kB @ 846.2kB/s  0.1s
ncurses                                            935.9kB @   1.7MB/s  0.1s
tk                                                   3.6MB @   6.2MB/s  0.2s
libgcc-ng                                            5.6MB @   9.7MB/s  0.2s
charset-normalizer                                  45.5kB @  77.8kB/s  0.0s
urllib3                                            183.4kB @ 285.0kB/s  0.1s
pip                                                  2.8MB @   3.9MB/s  0.1s
openssl                                              5.4MB @   7.5MB/s  0.1s
libuuid                                             28.1kB @  31.2kB/s  0.7s
python                                              28.1MB @  24.4MB/s  0.7s

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To activate this environment, use

     $ mamba activate mtest2

To deactivate an active environment, use

     $ mamba deactivate

(base) jjimenezluna@LAPTOP-DVESE69K:~$ conda activate mtest2
(mtest2) jjimenezluna@LAPTOP-DVESE69K:~$ mamba install molskill=*=py310* -c msr-ai4science -c conda-forge

Looking for: ['molskill=[build=py310*]']

msr-ai4science/linux-64 (check zst)                 Checked  0.3s
msr-ai4science/noarch (check zst)                   Checked  0.2s
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
pkgs/main/linux-64                                          Using cache
pkgs/main/noarch                                            Using cache
pkgs/r/linux-64                                             Using cache
pkgs/r/noarch                                               Using cache
pytorch/linux-64                                            Using cache
pytorch/noarch                                              Using cache
msr-ai4science/noarch                              116.0 B @ 454.0 B/s  0.3s
msr-ai4science/linux-64                              1.5kB @   4.0kB/s  0.4s

Pinned packages:
  - python 3.10.*

Transaction

  Prefix: /home/jjimenezluna/miniconda3/envs/mtest2

  Updating specs:

   - molskill=*[build=py310*]
   - ca-certificates
   - certifi
   - openssl

  Package                        Version  Build                        Channel              Size
──────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────────────────────────

  + python_abi                      3.10  2_cp310                      conda-forge           4kB
  + chardet                        5.2.0  py310hff52083_1              conda-forge         247kB
  + xorg-libxdmcp                  1.1.3  h7f98852_0                   conda-forge          19kB
  + pthread-stubs                    0.4  h36c2ea0_1001                conda-forge           6kB
  + libexpat                       2.6.2  h59595ed_0                   conda-forge          74kB
  + libiconv                        1.17  hd590300_2                   conda-forge         706kB
  + libdeflate                      1.17  h0b41bf4_0                   conda-forge          65kB
  + markupsafe                     2.1.5  py310h2372a71_0              conda-forge          24kB
  + xorg-libxau                   1.0.11  hd590300_0                   conda-forge          14kB
  + libwebp-base                   1.4.0  hd590300_0                   conda-forge         439kB
  + jpeg                              9e  h0b41bf4_3                   conda-forge         240kB
  + unicodedata2                  15.1.0  py310h2372a71_0              conda-forge         374kB
  + libbrotlicommon                1.1.0  hd590300_1                   conda-forge          69kB
  + yaml                           0.2.5  h7f98852_2                   conda-forge          89kB
  + libgfortran5                  14.1.0  hc5f4f2c_0                   conda-forge           1MB
  + c-ares                        1.32.3  h4bc722e_0                   conda-forge         180kB
  + libuv                         1.48.0  hd590300_0                   conda-forge         900kB
  + sleef                          3.6.1  h3400bea_1                   conda-forge         998kB
  + expat                          2.6.2  h59595ed_0                   conda-forge         138kB
  + libxcb                          1.16  hd590300_0                   conda-forge         395kB
  + libbrotlienc                   1.1.0  hd590300_1                   conda-forge         283kB
  + libbrotlidec                   1.1.0  hd590300_1                   conda-forge          33kB
  + pyyaml                         6.0.2  py310h5b4e0ec_0              conda-forge         181kB
  + libgfortran-ng                14.1.0  h69a702a_0                   conda-forge          50kB
  + lerc                             3.0  h9c3ff4c_0                   conda-forge         222kB
  + lz4-c                          1.9.4  hcb278e6_0                   conda-forge         143kB
  + greenlet                       3.0.3  py310hc6cd4ac_0              conda-forge         211kB
  + pixman                        0.43.2  h59595ed_0                   conda-forge         387kB
  + icu                             73.2  h59595ed_0                   conda-forge          12MB
  + qhull                         2020.2  h434a139_5                   conda-forge         553kB
  + kiwisolver                     1.4.5  py310hd41b1e2_1              conda-forge          73kB
  + re2                       2022.04.01  h27087fc_0                   conda-forge         217kB
  + cudatoolkit                   11.8.0  h4ba93d1_13                  conda-forge         716MB
  + libabseil                 20240116.2  cxx17_he02047a_1             conda-forge           1MB
  + tensorboard-data-server        0.7.0  py310h75e40e8_1              conda-forge           5MB
  + brotli-bin                     1.1.0  hd590300_1                   conda-forge          19kB
  + libopenblas                   0.3.27  pthreads_hac2b453_1          conda-forge           6MB
  + brotli                         1.1.0  hd590300_1                   conda-forge          19kB
  + libblas                        3.9.0  23_linux64_openblas          conda-forge          15kB
  + liblapack                      3.9.0  23_linux64_openblas          conda-forge          15kB
  + libcblas                       3.9.0  23_linux64_openblas          conda-forge          15kB
  + numpy                         1.26.4  py310hb13e2d6_0              conda-forge           7MB
  + contourpy                      1.2.1  py310hd41b1e2_0              conda-forge         242kB
  + libboost-python               1.82.0  py310hcb52e73_6              conda-forge         119kB
  + scipy                         1.14.0  py310h93e2701_1              conda-forge          17MB
  + future                         1.0.0  pyhd8ed1ab_0                 conda-forge         364kB
  + packaging                       24.1  pyhd8ed1ab_0                 conda-forge          50kB
  + fsspec                      2024.6.1  pyhff2d567_0                 conda-forge         133kB
  + pydeprecate                    0.3.2  pyhd8ed1ab_0                 conda-forge          13kB
  + networkx                         3.3  pyhd8ed1ab_1                 conda-forge           1MB
  + typing_extensions             4.12.2  pyha770c72_0                 conda-forge          40kB
  + nomkl                            1.0  h5ca1d4c_0                   conda-forge           4kB
  + colorama                       0.4.6  pyhd8ed1ab_0                 conda-forge          25kB
  + absl-py                        2.1.0  pyhd8ed1ab_0                 conda-forge         107kB
  + six                           1.16.0  pyh6c4a22f_0                 conda-forge          14kB
  + mpmath                         1.3.0  pyhd8ed1ab_0                 conda-forge         438kB
  + zipp                          3.19.2  pyhd8ed1ab_0                 conda-forge          21kB
  + threadpoolctl                  3.5.0  pyhc1e730c_0                 conda-forge          24kB
  + filelock                      3.15.4  pyhd8ed1ab_0                 conda-forge          18kB
  + python-tzdata                 2024.1  pyhd8ed1ab_0                 conda-forge         144kB
  + pytz                          2024.1  pyhd8ed1ab_0                 conda-forge         189kB
  + cycler                        0.12.1  pyhd8ed1ab_0                 conda-forge          13kB
  + pyparsing                      3.1.2  pyhd8ed1ab_0                 conda-forge          89kB
  + munkres                        1.1.4  pyh9f0ad1d_0                 conda-forge          12kB
  + joblib                         1.4.2  pyhd8ed1ab_0                 conda-forge         220kB
  + jinja2                         3.1.4  pyhd8ed1ab_0                 conda-forge         112kB
  + werkzeug                       3.0.3  pyhd8ed1ab_0                 conda-forge         243kB
  + lightning-utilities           0.11.6  pyhd8ed1ab_0                 conda-forge          28kB
  + typing-extensions             4.12.2  hd8ed1ab_0                   conda-forge          10kB
  + tqdm                          4.66.5  pyhd8ed1ab_0                 conda-forge          90kB
  + python-dateutil                2.9.0  pyhd8ed1ab_0                 conda-forge         223kB
  + sympy                         1.13.0  pyh04b8f61_3                 conda-forge           5MB
  + importlib-metadata             8.2.0  pyha770c72_0                 conda-forge          28kB
  + markdown                         3.6  pyhd8ed1ab_0                 conda-forge          78kB
  + pcre2                          10.42  hebb0a14_1                   pkgs/main             1MB
  + libpng                        1.6.39  h5eee18b_0                   pkgs/main           311kB
  + zstd                           1.5.5  hc292b87_2                   pkgs/main           658kB
  + libxml2                       2.13.1  hfdd30dd_2                   pkgs/main           757kB
  + libprotobuf                   4.25.3  he621ea3_0                   pkgs/main             3MB
  + libglib                       2.78.4  hdc74915_0                   pkgs/main             2MB
  + freetype                      2.12.1  h4a9f257_0                   pkgs/main           641kB
  + libtiff                        4.5.1  h6a678d5_0                   pkgs/main           546kB
  + libboost                      1.82.0  h109eef0_2                   pkgs/main            20MB
  + libgrpc                       1.62.2  h2d74bed_0                   pkgs/main             8MB
  + glib-tools                    2.78.4  h6a678d5_0                   pkgs/main           118kB
  + fontconfig                    2.14.1  h55d465d_3                   pkgs/main           288kB
  + openjpeg                       2.5.2  he7f1fd0_0                   pkgs/main           380kB
  + grpcio                        1.62.2  py310h6a678d5_0              pkgs/main             1MB
  + glib                          2.78.4  h6a678d5_0                   pkgs/main           520kB
  + cairo                         1.16.0  hb05425b_5                   pkgs/main             1MB
  + fonttools                     4.53.1  py310h5b4e0ec_0              conda-forge           2MB
  + scikit-learn                   1.5.1  py310h146d792_0              conda-forge           9MB
  + sqlalchemy                    2.0.32  py310h5b4e0ec_0              conda-forge           3MB
  + pandas                         2.2.2  py310hf9f9076_1              conda-forge          13MB
  + protobuf                      4.25.3  py310ha8c1f0e_0              conda-forge         332kB
  + libtorch                       2.3.1  cpu_generic_h970db74_0       conda-forge          50MB
  + lcms2                           2.15  hfd0df8a_0                   conda-forge         241kB
  + pycairo                       1.25.0  py310hda9f760_1              conda-forge         115kB
  + pytorch                        2.3.1  cpu_generic_py310ha4c588e_0  conda-forge          30MB
  + freetype-py                    2.3.0  pyhd8ed1ab_0                 conda-forge          59kB
  + tensorboard                   2.17.0  pyhd8ed1ab_0                 conda-forge           5MB
  + torchmetrics             1.4.0.post0  pyhd8ed1ab_0                 conda-forge         350kB
  + rlpycairo                      0.2.0  pyhd8ed1ab_0                 conda-forge          15kB
  + pytorch-lightning              1.6.3  pyhd8ed1ab_0                 conda-forge         330kB
  + pillow                        10.4.0  py310h5eee18b_0              pkgs/main           823kB
  + reportlab                      4.2.2  py310hc51659f_0              conda-forge           2MB
  + matplotlib-base                3.9.1  py310hf02ac8c_2              conda-forge           7MB
  + rdkit                      2023.03.3  py310hb79e901_1              conda-forge          36MB
  + molskill                         1.2  py310h8e7c8fa_3              msr-ai4science       55kB

  Change:
──────────────────────────────────────────────────────────────────────────────────────────────────

  - _libgcc_mutex                    0.1  main                         pkgs/main          Cached
  + _libgcc_mutex                    0.1  conda_forge                  conda-forge           3kB

  Upgrade:
──────────────────────────────────────────────────────────────────────────────────────────────────

  - ca-certificates             2024.7.2  h06a4308_0                   pkgs/main          Cached
  + ca-certificates             2024.7.4  hbcca054_0                   conda-forge         155kB
  - libgomp                       11.2.0  h1234567_1                   pkgs/main          Cached
  + libgomp                       14.1.0  h77fa898_0                   conda-forge         457kB
  - libgcc-ng                     11.2.0  h1234567_1                   pkgs/main          Cached
  + libgcc-ng                     14.1.0  h77fa898_0                   conda-forge         842kB
  - libstdcxx-ng                  11.2.0  h1234567_1                   pkgs/main          Cached
  + libstdcxx-ng                  14.1.0  hc0a3c3a_0                   conda-forge           4MB
  - openssl                       3.0.14  h5eee18b_0                   pkgs/main          Cached
  + openssl                        3.3.1  h4bc722e_2                   conda-forge           3MB

  Downgrade:
──────────────────────────────────────────────────────────────────────────────────────────────────

  - setuptools                    72.1.0  py310h06a4308_0              pkgs/main          Cached
  + setuptools                    59.5.0  py310hff52083_0              conda-forge           1MB
  - _openmp_mutex                    5.1  1_gnu                        pkgs/main          Cached
  + _openmp_mutex                    4.5  2_gnu                        conda-forge          24kB

  Summary:

  Install: 109 packages
  Change: 1 packages
  Upgrade: 5 packages
  Downgrade: 2 packages

  Total download: 992MB

──────────────────────────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] Y
python_abi                                           4.1kB @  28.9kB/s  0.1s
_libgcc_mutex                                        2.6kB @  15.9kB/s  0.2s
ca-certificates                                    154.9kB @ 819.9kB/s  0.2s
chardet                                            246.6kB @   1.2MB/s  0.2s
libexpat                                            73.7kB @ 370.9kB/s  0.1s
markupsafe                                          24.5kB @ 115.2kB/s  0.1s
libgomp                                            456.9kB @   1.9MB/s  0.2s
yaml                                                89.1kB @ 350.6kB/s  0.1s
jpeg                                               240.4kB @ 930.4kB/s  0.1s
libgfortran5                                         1.5MB @   4.6MB/s  0.1s
libgfortran-ng                                      49.9kB @ 150.7kB/s  0.1s
openssl                                              2.9MB @   8.6MB/s  0.1s
libbrotlienc                                       282.5kB @ 820.8kB/s  0.1s
greenlet                                           211.0kB @ 586.6kB/s  0.1s
brotli-bin                                          19.0kB @  49.5kB/s  0.0s
qhull                                              552.9kB @   1.3MB/s  0.1s
libblas                                             14.9kB @  32.1kB/s  0.1s
typing_extensions                                   39.9kB @  75.5kB/s  0.1s
numpy                                                7.0MB @  12.0MB/s  0.2s
absl-py                                            107.3kB @ 182.1kB/s  0.1s
python-tzdata                                      144.0kB @ 226.2kB/s  0.0s
zipp                                                20.9kB @  32.5kB/s  0.1s
jinja2                                             111.6kB @ 160.0kB/s  0.1s
scipy                                               16.7MB @  22.6MB/s  0.4s
typing-extensions                                   10.1kB @  13.5kB/s  0.1s
fsspec                                             133.1kB @ 166.4kB/s  0.4s
sympy                                                4.5MB @   5.2MB/s  0.1s
pcre2                                                1.4MB @   1.5MB/s  0.2s
openjpeg                                           379.8kB @ 406.5kB/s  0.0s
cairo                                                1.2MB @   1.2MB/s  0.1s
pyparsing                                           89.5kB @  87.4kB/s  0.4s
libxml2                                            757.1kB @ 731.1kB/s  0.2s
sqlalchemy                                           2.8MB @   2.2MB/s  0.3s
libboost                                            20.5MB @  15.4MB/s  0.5s
pytorch-lightning                                  329.9kB @ 225.4kB/s  0.2s
_openmp_mutex                                       23.6kB @  15.2kB/s  0.1s
matplotlib-base                                      7.0MB @   4.4MB/s  0.3s
pthread-stubs                                        5.6kB @   3.5kB/s  0.1s
xorg-libxau                                         14.5kB @   8.8kB/s  0.0s
libbrotlicommon                                     69.4kB @  41.3kB/s  0.1s
sleef                                              998.1kB @ 568.4kB/s  0.1s
lerc                                               221.6kB @ 122.0kB/s  0.1s
libxcb                                             394.9kB @ 191.9kB/s  0.4s
pytorch                                             30.1MB @  14.5MB/s  1.0s
brotli                                              19.4kB @   9.0kB/s  0.1s
icu                                                 12.1MB @   5.6MB/s  0.4s
libabseil                                            1.3MB @ 568.7kB/s  0.2s
packaging                                           50.3kB @  22.3kB/s  0.1s
contourpy                                          241.9kB @ 106.3kB/s  0.1s
nomkl                                                3.8kB @   1.7kB/s  0.1s
mpmath                                             438.3kB @ 190.0kB/s  0.1s
joblib                                             219.7kB @  92.8kB/s  0.1s
tqdm                                                89.5kB @  37.5kB/s  0.1s
markdown                                            78.3kB @  32.3kB/s  0.1s
libprotobuf                                          3.0MB @   1.2MB/s  0.2s
glib                                               519.8kB @ 196.8kB/s  0.1s
pytz                                               188.5kB @  71.2kB/s  0.4s
libgrpc                                              8.4MB @   3.1MB/s  0.3s
pycairo                                            115.2kB @  39.5kB/s  0.3s
rlpycairo                                           14.9kB @   5.1kB/s  0.2s
xorg-libxdmcp                                       19.1kB @   6.4kB/s  0.1s
libwebp-base                                       439.0kB @ 141.1kB/s  0.1s
pandas                                              13.0MB @   4.2MB/s  0.5s
libbrotlidec                                        32.8kB @  10.3kB/s  0.1s
pixman                                             386.8kB @ 118.6kB/s  0.1s
molskill                                            54.5kB @  16.6kB/s  0.4s
libcblas                                            14.8kB @   4.4kB/s  0.1s
tensorboard-data-server                              4.8MB @   1.4MB/s  0.2s
pydeprecate                                         13.5kB @   3.9kB/s  0.1s
libuv                                              900.0kB @ 260.1kB/s  0.3s
six                                                 14.3kB @   4.1kB/s  0.1s
lightning-utilities                                 27.5kB @   7.7kB/s  0.1s
cycler                                              13.5kB @   3.8kB/s  0.1s
libtorch                                            50.0MB @  13.8MB/s  2.6s
libpng                                             311.2kB @  86.1kB/s  0.1s
glib-tools                                         118.0kB @  32.5kB/s  0.1s
libtiff                                            545.8kB @ 149.9kB/s  0.1s
freetype-py                                         58.9kB @  16.1kB/s  0.1s
pillow                                             823.3kB @ 223.7kB/s  0.1s
libdeflate                                          65.0kB @  17.3kB/s  0.1s
re2                                                216.8kB @  57.2kB/s  0.1s
libstdcxx-ng                                         3.9MB @   1.0MB/s  0.1s
setuptools                                           1.1MB @ 282.1kB/s  0.2s
threadpoolctl                                       23.5kB @   6.1kB/s  0.1s
future                                             364.1kB @  94.6kB/s  0.1s
werkzeug                                           242.9kB @  63.1kB/s  0.1s
fontconfig                                         288.1kB @  72.0kB/s  0.2s
zstd                                               658.0kB @ 163.3kB/s  0.2s
tensorboard                                          5.2MB @   1.3MB/s  0.2s
scikit-learn                                         9.2MB @   2.3MB/s  0.2s
kiwisolver                                          73.1kB @  17.8kB/s  0.0s
networkx                                             1.2MB @ 286.0kB/s  0.1s
python-dateutil                                    222.7kB @  53.6kB/s  0.1s
expat                                              137.6kB @  33.1kB/s  0.1s
libiconv                                           705.8kB @ 168.9kB/s  0.2s
protobuf                                           332.4kB @  78.4kB/s  0.1s
c-ares                                             179.7kB @  42.4kB/s  0.1s
lcms2                                              240.8kB @  56.7kB/s  0.1s
importlib-metadata                                  28.1kB @   6.5kB/s  0.1s
colorama                                            25.2kB @   5.8kB/s  0.1s
fonttools                                            2.4MB @ 524.8kB/s  0.2s
libopenblas                                          5.6MB @   1.2MB/s  0.3s
libboost-python                                    119.1kB @  26.1kB/s  0.1s
pyyaml                                             181.2kB @  39.7kB/s  0.1s
freetype                                           640.8kB @ 138.1kB/s  0.5s
libglib                                              1.6MB @ 331.7kB/s  0.2s
reportlab                                            2.4MB @ 496.9kB/s  0.2s
liblapack                                           14.8kB @   3.1kB/s  0.1s
lz4-c                                              143.4kB @  29.7kB/s  0.1s
grpcio                                               1.1MB @ 218.5kB/s  0.1s
torchmetrics                                       350.1kB @  71.3kB/s  0.2s
libgcc-ng                                          842.1kB @ 171.1kB/s  0.1s
filelock                                            17.6kB @   3.5kB/s  0.1s
unicodedata2                                       374.1kB @  75.0kB/s  0.1s
munkres                                             12.5kB @   2.5kB/s  0.1s
rdkit                                               36.3MB @   6.6MB/s  1.2s
cudatoolkit                                        715.6MB @  58.1MB/s 12.0s

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: / By downloading and using the CUDA Toolkit conda packages, you accept the terms and conditions of the CUDA End User License Agreement (EULA): https://docs.nvidia.com/cuda/eula/index.html

done
vincenzo-palmacci commented 3 months ago

I think I found the problem. When installing Molskill my mamba retrieves the chaced NumPy version which in my case is 2.0.1 . Given that to my knowledge conda doesn't have a "no_cache" option, for me downgrading the NumPy version worked fine. Screenshot 2024-08-12 at 10 20 14