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MolecularAI / REINVENT4

AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.
Apache License 2.0
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ImportError: libcudnn.so.8: cannot open shared object file: No such file or directory #67

Closed Evert-Homan closed 6 months ago

Evert-Homan commented 6 months ago

Hi,

Ran through the installation (Ubuntu 22.04) and noted a number of warnings in red when issuing

pip install -r requirements-linux-64.lock

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
alembic 1.12.1 requires Mako, which is not installed.
bleach 6.0.0 requires webencodings, which is not installed.
jupyterhub 4.0.2 requires oauthlib>=3.0, which is not installed.
prodec 1.0.2.post5 requires psutil, which is not installed.
requests-oauthlib 1.3.1 requires oauthlib>=3.0.0, which is not installed.
swifter 1.4.0 requires psutil>=5.6.6, which is not installed.
botocore 1.34.51 requires urllib3<2.1,>=1.25.4; python_version >= "3.10", but you have urllib3 2.2.1 which is incompatible.
datasets 2.14.5 requires dill<0.3.8,>=0.3.0, but you have dill 0.3.8 which is incompatible.
datasets 2.14.5 requires fsspec[http]<2023.9.0,>=2023.1.0, but you have fsspec 2024.3.1 which is incompatible.
google-api-core 2.18.0 requires protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0.dev0,>=3.19.5, but you have protobuf 5.26.1 which is incompatible.
googleapis-common-protos 1.63.0 requires protobuf!=3.20.0,!=3.20.1,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0.dev0,>=3.19.5, but you have protobuf 5.26.1 which is incompatible.
mordred 1.2.0 requires networkx==2.*, but you have networkx 3.3 which is incompatible.
numba 0.55.2 requires numpy<1.23,>=1.18, but you have numpy 1.26.4 which is incompatible.
plotly-resampler 0.8.2rc3 requires pandas<2.0.0,>=1.3.5, but you have pandas 2.2.2 which is incompatible.
proto-plus 1.23.0 requires protobuf<5.0.0dev,>=3.19.0, but you have protobuf 5.26.1 which is incompatible.
qsprpred 2.1.0 requires numpy<1.24.0,>=1.19, but you have numpy 1.26.4 which is incompatible.
sklearn-json 0.1.7 requires scikit-learn<1.2.2,>=0.21.3, but you have scikit-learn 1.2.2 which is incompatible.
sktime 0.13.4 requires numpy<1.23,>=1.21.0, but you have numpy 1.26.4 which is incompatible.
sktime 0.13.4 requires pandas<1.6.0,>=1.1.0, but you have pandas 2.2.2 which is incompatible.
sktime 0.13.4 requires scikit-learn<1.2.0,>=0.24.0, but you have scikit-learn 1.2.2 which is incompatible.
sktime 0.13.4 requires scipy<1.9.0, but you have scipy 1.13.0 which is incompatible.
tensorflow 2.14.0 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0dev,>=3.20.3, but you have protobuf 5.26.1 which is incompatible.
tensorflow 2.14.0 requires tensorboard<2.15,>=2.14, but you have tensorboard 2.16.2 which is incompatible.
torchaudio 2.0.2+cu117 requires torch==2.0.1, but you have torch 2.2.1+cu121 which is incompatible.
torchdata 0.6.1 requires torch==2.0.1, but you have torch 2.2.1+cu121 which is incompatible.

but moved on anyway. When testing I get:

reinvent --help
Traceback (most recent call last):
  File "/home/evehom/miniforge3/envs/reinvent4/bin/reinvent", line 5, in <module>
    from reinvent.Reinvent import main
  File "/home/evehom/Data/CompChem/Python/REINVENT4/reinvent/__init__.py", line 9, in <module>
    from reinvent import models
  File "/home/evehom/Data/CompChem/Python/REINVENT4/reinvent/models/__init__.py", line 3, in <module>
    from .reinvent.models.model import Model as ReinventModel
  File "/home/evehom/Data/CompChem/Python/REINVENT4/reinvent/models/reinvent/models/model.py", line 11, in <module>
    import torch
  File "/home/evehom/miniforge3/envs/reinvent4/lib/python3.10/site-packages/torch/__init__.py", line 237, in <module>
    from torch._C import *  # noqa: F403
ImportError: libcudnn.so.8: cannot open shared object file: No such file or directory
/local/cuda/lib64 ls libcudnn*
libcudnn_adv.so           libcudnn_engines_precompiled.so                libcudnn_graph.so               libcudnn_ops.so
libcudnn_adv.so.9         libcudnn_engines_precompiled.so.9              libcudnn_graph.so.9             libcudnn_ops.so.9
libcudnn_adv.so.9.1.0     libcudnn_engines_precompiled.so.9.1.0          libcudnn_graph.so.9.1.0         libcudnn_ops.so.9.1.0
libcudnn_adv_static.a     libcudnn_engines_precompiled_static.a          libcudnn_graph_static.a         libcudnn_ops_static.a
libcudnn_adv_static_v9.a  libcudnn_engines_precompiled_static_v9.a       libcudnn_graph_static_v9.a      libcudnn_ops_static_v9.a
libcudnn_cnn.so           libcudnn_engines_runtime_compiled.so           libcudnn_heuristic.so           libcudnn.so
libcudnn_cnn.so.9         libcudnn_engines_runtime_compiled.so.9         libcudnn_heuristic.so.9         libcudnn.so.9
libcudnn_cnn.so.9.1.0     libcudnn_engines_runtime_compiled.so.9.1.0     libcudnn_heuristic.so.9.1.0     libcudnn.so.9.1.0
libcudnn_cnn_static.a     libcudnn_engines_runtime_compiled_static.a     libcudnn_heuristic_static.a
libcudnn_cnn_static_v9.a  libcudnn_engines_runtime_compiled_static_v9.a  libcudnn_heuristic_static_v9.a
nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2024 NVIDIA Corporation
Built on Thu_Mar_28_02:18:24_PDT_2024
Cuda compilation tools, release 12.4, V12.4.131
Build cuda_12.4.r12.4/compiler.34097967_0

Grateful for any pointers on how to get this working. As a Python novice I have difficulties understanding why newer versions of packages are not backwards compatible.

Thanks/Evert

halx commented 6 months ago

Hi,

many thanks for your interest in REINVENT and welcome to the community!

I think I will need much more details here. Have you created a virtual environment before carrying out this install? Have you started from a freshly created environment or are you trying to install over a previous one? I ask this because the packages that your pip is trying to install are actually not in requirements-linux-64.lock or for different versions.

Dependency problems are manyfold but primarily down to the fact that pip, conda, etc. are not consistent distributions but rather random selections of packages from random people. You may find indeed that newer packages suddenly are dependent on older software than before and many other odd things. But what I see here seems to be a problem of forward compatibility e.g. you have a new(er) torch install but are trying to install and older version of tensorflow.

Many thanks, Hannes.

Evert-Homan commented 6 months ago

Hi, and thanks for your swift response. I started from scratch, even wiped miniconda3 and all environments, and reinstalled it. Then I updated conda. Then I followed the installation instructions to the letter, but get the same error message when testing. I do all this on Ubuntu 22.04. On WSL2/Debian I can get it to work without errors.

Any ideas? Thanks for your patience/Evert

git clone https://github.com/MolecularAI/REINVENT4.git
Cloning into 'REINVENT4'...
remote: Enumerating objects: 1942, done.
remote: Counting objects: 100% (578/578), done.
remote: Compressing objects: 100% (304/304), done.
remote: Total 1942 (delta 296), reused 495 (delta 267), pack-reused 1364
Receiving objects: 100% (1942/1942), 1.27 GiB | 17.33 MiB/s, done.
Resolving deltas: 100% (779/779), done.
Updating files: 100% (548/548), done.
 evehom  ~  Data  CompChem  Python  conda create --name reinvent4 python=3.10
conda activate reinvent4
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/evehom/miniconda3/envs/reinvent4

  added / updated specs:
    - python=3.10

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-hd590300_5 
  ca-certificates    conda-forge/linux-64::ca-certificates-2024.2.2-hbcca054_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.40-h55db66e_0 
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-13.2.0-hc881cc4_6 
  libgomp            conda-forge/linux-64::libgomp-13.2.0-hc881cc4_6 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0 
  libsqlite          conda-forge/linux-64::libsqlite-3.45.3-h2797004_0 
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.2.13-hd590300_5 
  ncurses            conda-forge/linux-64::ncurses-6.4.20240210-h59595ed_0 
  openssl            conda-forge/linux-64::openssl-3.2.1-hd590300_1 
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 
  python             conda-forge/linux-64::python-3.10.14-hd12c33a_0_cpython 
  readline           conda-forge/linux-64::readline-8.2-h8228510_1 
  setuptools         conda-forge/noarch::setuptools-69.5.1-pyhd8ed1ab_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0 
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0 

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate reinvent4
#
# To deactivate an active environment, use
#
#     $ conda deactivate

 evehom  (e) reinvent4  ~  Data  CompChem  Python  cd REINVENT4/
 evehom  (e) reinvent4   main  …  CompChem  Python  REINVENT4  pip install -r requirements-linux-64.lock
Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cu121, https://pypi.anaconda.org/OpenEye/simple
Collecting absl-py==2.1.0 (from -r requirements-linux-64.lock (line 10))
  Using cached absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Requirement already satisfied: alabaster==0.7.16 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 12)) (0.7.16)
Requirement already satisfied: annotated-types==0.6.0 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 14)) (0.6.0)
Collecting babel==2.14.0 (from -r requirements-linux-64.lock (line 16))
  Using cached Babel-2.14.0-py3-none-any.whl.metadata (1.6 kB)
Requirement already satisfied: blinker==1.7.0 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 18)) (1.7.0)
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Requirement already satisfied: charset-normalizer==3.3.2 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 22)) (3.3.2)
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  Using cached chemprop-1.5.2-py3-none-any.whl
Requirement already satisfied: click==8.1.7 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 26)) (8.1.7)
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  Using cached idna-3.7-py3-none-any.whl.metadata (9.9 kB)
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  Using cached https://download.pytorch.org/whl/Jinja2-3.1.3-py3-none-any.whl (133 kB)
Collecting joblib==1.4.0 (from -r requirements-linux-64.lock (line 77))
  Using cached joblib-1.4.0-py3-none-any.whl.metadata (5.4 kB)
Collecting kiwisolver==1.4.5 (from -r requirements-linux-64.lock (line 79))
  Using cached kiwisolver-1.4.5-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.4 kB)
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  Using cached Markdown-3.6-py3-none-any.whl.metadata (7.0 kB)
Requirement already satisfied: markupsafe==2.1.5 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 83)) (2.1.5)
Collecting matplotlib==3.8.4 (from -r requirements-linux-64.lock (line 87))
  Using cached matplotlib-3.8.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
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Requirement already satisfied: mypy-extensions==1.0.0 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 99)) (1.0.0)
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  Using cached networkx-3.3-py3-none-any.whl.metadata (5.1 kB)
Collecting numpy==1.26.4 (from -r requirements-linux-64.lock (line 105))
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Requirement already satisfied: nvidia-cuda-cupti-cu12==12.1.105 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 126)) (12.1.105)
Requirement already satisfied: nvidia-cuda-nvrtc-cu12==12.1.105 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 128)) (12.1.105)
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Requirement already satisfied: nvidia-cusolver-cu12==11.4.5.107 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 138)) (11.4.5.107)
Requirement already satisfied: nvidia-cusparse-cu12==12.1.0.106 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 140)) (12.1.0.106)
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Requirement already satisfied: nvidia-nvtx-cu12==12.1.105 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 150)) (12.1.105)
WARNING: Cache entry deserialization failed, entry ignored
Collecting openeye-toolkits==2023.2.3 (from -r requirements-linux-64.lock (line 152))
  Downloading https://pypi.anaconda.org/openeye/simple/openeye-toolkits/2023.2.3/OpenEye_toolkits-2023.2.3-py39.py310.py311-none-manylinux_2_28_x86_64.whl (285.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 285.2/285.2 MB 4.3 MB/s eta 0:00:00
Requirement already satisfied: packaging==24.0 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 154)) (24.0)
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  Using cached pandas-2.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Requirement already satisfied: pandas-flavor==0.6.0 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 167)) (0.6.0)
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Requirement already satisfied: pygments==2.17.2 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 195)) (2.17.2)
Collecting pyparsing==3.1.2 (from -r requirements-linux-64.lock (line 197))
  Using cached pyparsing-3.1.2-py3-none-any.whl.metadata (5.1 kB)
Collecting pytest==8.1.1 (from -r requirements-linux-64.lock (line 199))
  Using cached pytest-8.1.1-py3-none-any.whl.metadata (7.6 kB)
Collecting pytest-mock==3.14.0 (from -r requirements-linux-64.lock (line 203))
  Using cached pytest_mock-3.14.0-py3-none-any.whl.metadata (3.8 kB)
Collecting python-dateutil==2.9.0.post0 (from -r requirements-linux-64.lock (line 205))
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Requirement already satisfied: python-dotenv==1.0.1 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 209)) (1.0.1)
Requirement already satisfied: pytz==2024.1 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 211)) (2024.1)
Collecting pyyaml==6.0.1 (from -r requirements-linux-64.lock (line 213))
  Using cached PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting rdkit==2023.9.5 (from -r requirements-linux-64.lock (line 215))
  Using cached rdkit-2023.9.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.9 kB)
Requirement already satisfied: requests==2.31.0 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 219)) (2.31.0)
Collecting requests-mock==1.12.1 (from -r requirements-linux-64.lock (line 224))
  Using cached requests_mock-1.12.1-py2.py3-none-any.whl.metadata (4.1 kB)
Collecting scikit-learn==1.2.2 (from -r requirements-linux-64.lock (line 226))
  Using cached scikit_learn-1.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting scipy==1.13.0 (from -r requirements-linux-64.lock (line 230))
  Using cached scipy-1.13.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting six==1.16.0 (from -r requirements-linux-64.lock (line 237))
  Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Requirement already satisfied: snowballstemmer==2.2.0 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 243)) (2.2.0)
Requirement already satisfied: sphinx==7.2.6 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 245)) (7.2.6)
Requirement already satisfied: sphinxcontrib-applehelp==1.0.8 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 247)) (1.0.8)
Requirement already satisfied: sphinxcontrib-devhelp==1.0.6 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 249)) (1.0.6)
Requirement already satisfied: sphinxcontrib-htmlhelp==2.0.5 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 251)) (2.0.5)
Requirement already satisfied: sphinxcontrib-jsmath==1.0.1 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 253)) (1.0.1)
Requirement already satisfied: sphinxcontrib-qthelp==1.0.7 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 255)) (1.0.7)
Requirement already satisfied: sphinxcontrib-serializinghtml==1.1.10 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 257)) (1.1.10)
Requirement already satisfied: sympy==1.12 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 259)) (1.12)
Collecting tenacity==8.2.3 (from -r requirements-linux-64.lock (line 261))
  Using cached tenacity-8.2.3-py3-none-any.whl.metadata (1.0 kB)
Collecting tensorboard==2.16.2 (from -r requirements-linux-64.lock (line 263))
  Using cached tensorboard-2.16.2-py3-none-any.whl.metadata (1.6 kB)
Collecting tensorboard-data-server==0.7.2 (from -r requirements-linux-64.lock (line 265))
  Using cached tensorboard_data_server-0.7.2-py3-none-manylinux_2_31_x86_64.whl.metadata (1.1 kB)
Requirement already satisfied: tensorboardx==2.6.2.2 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 267)) (2.6.2.2)
Collecting threadpoolctl==3.4.0 (from -r requirements-linux-64.lock (line 269))
  Using cached threadpoolctl-3.4.0-py3-none-any.whl.metadata (13 kB)
Requirement already satisfied: tomli==2.0.1 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 271)) (2.0.1)
Collecting torch==2.2.1+cu121 (from -r requirements-linux-64.lock (line 275))
  Using cached https://download.pytorch.org/whl/cu121/torch-2.2.1%2Bcu121-cp310-cp310-linux_x86_64.whl (757.3 MB)
Collecting torchvision==0.17.1+cu121 (from -r requirements-linux-64.lock (line 280))
  Using cached https://download.pytorch.org/whl/cu121/torchvision-0.17.1%2Bcu121-cp310-cp310-linux_x86_64.whl (7.0 MB)
Collecting tqdm==4.66.2 (from -r requirements-linux-64.lock (line 282))
  Using cached tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)
Collecting triton==2.2.0 (from -r requirements-linux-64.lock (line 287))
  Using cached https://download.pytorch.org/whl/triton-2.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (167.9 MB)
Collecting typed-argument-parser==1.10.0 (from -r requirements-linux-64.lock (line 289))
  Using cached typed_argument_parser-1.10.0-py3-none-any.whl
Collecting typing-extensions==4.11.0 (from -r requirements-linux-64.lock (line 291))
  Using cached typing_extensions-4.11.0-py3-none-any.whl.metadata (3.0 kB)
Requirement already satisfied: typing-inspect==0.9.0 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 298)) (0.9.0)
Requirement already satisfied: tzdata==2024.1 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 300)) (2024.1)
Collecting urllib3==2.2.1 (from -r requirements-linux-64.lock (line 302))
  Using cached urllib3-2.2.1-py3-none-any.whl.metadata (6.4 kB)
Requirement already satisfied: werkzeug==3.0.2 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 304)) (3.0.2)
Requirement already satisfied: xarray==2024.3.0 in /home/evehom/.local/lib/python3.10/site-packages (from -r requirements-linux-64.lock (line 308)) (2024.3.0)
Collecting xxhash==3.4.1 (from -r requirements-linux-64.lock (line 310))
  Using cached xxhash-3.4.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Requirement already satisfied: setuptools>=41.0.0 in /home/evehom/miniconda3/envs/reinvent4/lib/python3.10/site-packages (from tensorboard==2.16.2->-r requirements-linux-64.lock (line 263)) (69.5.1)
Using cached absl_py-2.1.0-py3-none-any.whl (133 kB)
Using cached Babel-2.14.0-py3-none-any.whl (11.0 MB)
Using cached certifi-2024.2.2-py3-none-any.whl (163 kB)
Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Using cached descriptastorus-2.6.1-py3-none-any.whl (1.1 MB)
Using cached dill-0.3.8-py3-none-any.whl (116 kB)
Using cached filelock-3.13.4-py3-none-any.whl (11 kB)
Using cached flask-3.0.3-py3-none-any.whl (101 kB)
Using cached fonttools-4.51.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
Using cached funcy-2.0-py2.py3-none-any.whl (30 kB)
Using cached future-1.0.0-py3-none-any.whl (491 kB)
Using cached grpcio-1.62.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.5 MB)
Using cached idna-3.7-py3-none-any.whl (66 kB)
Using cached iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Using cached joblib-1.4.0-py3-none-any.whl (301 kB)
Using cached kiwisolver-1.4.5-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
Using cached Markdown-3.6-py3-none-any.whl (105 kB)
Using cached matplotlib-3.8.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
Using cached mmpdb-2.1-py2.py3-none-any.whl (188 kB)
Using cached multiprocess-0.70.16-py310-none-any.whl (134 kB)
Using cached networkx-3.3-py3-none-any.whl (1.7 MB)
Using cached numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
Using cached pandas-2.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.0 MB)
Using cached pathos-0.3.2-py3-none-any.whl (82 kB)
Using cached pillow-10.3.0-cp310-cp310-manylinux_2_28_x86_64.whl (4.5 MB)
Using cached pluggy-1.4.0-py3-none-any.whl (20 kB)
Using cached pox-0.3.4-py3-none-any.whl (29 kB)
Using cached ppft-1.7.6.8-py3-none-any.whl (56 kB)
Using cached protobuf-5.26.1-cp37-abi3-manylinux2014_x86_64.whl (302 kB)
Using cached pydantic-2.7.0-py3-none-any.whl (407 kB)
Using cached pydantic_core-2.18.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
Using cached pyparsing-3.1.2-py3-none-any.whl (103 kB)
Using cached pytest-8.1.1-py3-none-any.whl (337 kB)
Using cached pytest_mock-3.14.0-py3-none-any.whl (9.9 kB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Using cached PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (705 kB)
Using cached rdkit-2023.9.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.4 MB)
Using cached requests_mock-1.12.1-py2.py3-none-any.whl (27 kB)
Using cached scikit_learn-1.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.6 MB)
Using cached scipy-1.13.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.6 MB)
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Using cached tenacity-8.2.3-py3-none-any.whl (24 kB)
Using cached tensorboard-2.16.2-py3-none-any.whl (5.5 MB)
Using cached tensorboard_data_server-0.7.2-py3-none-manylinux_2_31_x86_64.whl (6.6 MB)
Using cached threadpoolctl-3.4.0-py3-none-any.whl (17 kB)
Using cached tqdm-4.66.2-py3-none-any.whl (78 kB)
Using cached typing_extensions-4.11.0-py3-none-any.whl (34 kB)
Using cached urllib3-2.2.1-py3-none-any.whl (121 kB)
Using cached xxhash-3.4.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (194 kB)
Installing collected packages: mmpdb, funcy, xxhash, urllib3, typing-extensions, tqdm, threadpoolctl, tensorboard-data-server, tenacity, six, pyyaml, pyparsing, protobuf, ppft, pox, pluggy, pillow, openeye-toolkits, numpy, networkx, markdown, kiwisolver, joblib, jinja2, iniconfig, idna, grpcio, future, fonttools, filelock, dill, cycler, certifi, babel, absl-py, triton, tensorboard, scipy, rdkit, python-dateutil, pytest, pydantic-core, multiprocess, molvs, flask, typed-argument-parser, torch, scikit-learn, requests-mock, pytest-mock, pydantic, pathos, pandas, matplotlib, torchvision, descriptastorus, chemprop
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
alembic 1.12.1 requires Mako, which is not installed.
bleach 6.0.0 requires webencodings, which is not installed.
jupyterhub 4.0.2 requires oauthlib>=3.0, which is not installed.
prodec 1.0.2.post5 requires psutil, which is not installed.
requests-oauthlib 1.3.1 requires oauthlib>=3.0.0, which is not installed.
swifter 1.4.0 requires psutil>=5.6.6, which is not installed.
botocore 1.34.51 requires urllib3<2.1,>=1.25.4; python_version >= "3.10", but you have urllib3 2.2.1 which is incompatible.
datasets 2.14.5 requires dill<0.3.8,>=0.3.0, but you have dill 0.3.8 which is incompatible.
datasets 2.14.5 requires fsspec[http]<2023.9.0,>=2023.1.0, but you have fsspec 2024.3.1 which is incompatible.
google-api-core 2.18.0 requires protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0.dev0,>=3.19.5, but you have protobuf 5.26.1 which is incompatible.
googleapis-common-protos 1.63.0 requires protobuf!=3.20.0,!=3.20.1,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0.dev0,>=3.19.5, but you have protobuf 5.26.1 which is incompatible.
mordred 1.2.0 requires networkx==2.*, but you have networkx 3.3 which is incompatible.
numba 0.55.2 requires numpy<1.23,>=1.18, but you have numpy 1.26.4 which is incompatible.
plotly-resampler 0.8.2rc3 requires pandas<2.0.0,>=1.3.5, but you have pandas 2.2.2 which is incompatible.
proto-plus 1.23.0 requires protobuf<5.0.0dev,>=3.19.0, but you have protobuf 5.26.1 which is incompatible.
qsprpred 2.1.0 requires numpy<1.24.0,>=1.19, but you have numpy 1.26.4 which is incompatible.
sklearn-json 0.1.7 requires scikit-learn<1.2.2,>=0.21.3, but you have scikit-learn 1.2.2 which is incompatible.
sktime 0.13.4 requires numpy<1.23,>=1.21.0, but you have numpy 1.26.4 which is incompatible.
sktime 0.13.4 requires pandas<1.6.0,>=1.1.0, but you have pandas 2.2.2 which is incompatible.
sktime 0.13.4 requires scikit-learn<1.2.0,>=0.24.0, but you have scikit-learn 1.2.2 which is incompatible.
sktime 0.13.4 requires scipy<1.9.0, but you have scipy 1.13.0 which is incompatible.
tensorflow 2.14.0 requires protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0dev,>=3.20.3, but you have protobuf 5.26.1 which is incompatible.
tensorflow 2.14.0 requires tensorboard<2.15,>=2.14, but you have tensorboard 2.16.2 which is incompatible.
torchaudio 2.0.2+cu117 requires torch==2.0.1, but you have torch 2.2.1+cu121 which is incompatible.
torchdata 0.6.1 requires torch==2.0.1, but you have torch 2.2.1+cu121 which is incompatible.
Successfully installed absl-py-2.1.0 babel-2.14.0 certifi-2024.2.2 chemprop-1.5.2 cycler-0.12.1 descriptastorus-2.6.1 dill-0.3.8 filelock-3.13.4 flask-3.0.3 fonttools-4.51.0 funcy-2.0 future-1.0.0 grpcio-1.62.1 idna-3.7 iniconfig-2.0.0 jinja2-3.1.3 joblib-1.4.0 kiwisolver-1.4.5 markdown-3.6 matplotlib-3.8.4 mmpdb-2.1 molvs-0.1.1 multiprocess-0.70.16 networkx-3.3 numpy-1.26.4 openeye-toolkits-2023.2.3 pandas-2.2.2 pathos-0.3.2 pillow-10.3.0 pluggy-1.4.0 pox-0.3.4 ppft-1.7.6.8 protobuf-5.26.1 pydantic-2.7.0 pydantic-core-2.18.1 pyparsing-3.1.2 pytest-8.1.1 pytest-mock-3.14.0 python-dateutil-2.9.0.post0 pyyaml-6.0.1 rdkit-2023.9.5 requests-mock-1.12.1 scikit-learn-1.2.2 scipy-1.13.0 six-1.16.0 tenacity-8.2.3 tensorboard-2.16.2 tensorboard-data-server-0.7.2 threadpoolctl-3.4.0 torch-2.2.1+cu121 torchvision-0.17.1+cu121 tqdm-4.66.2 triton-2.2.0 typed-argument-parser-1.10.0 typing-extensions-4.11.0 urllib3-2.2.1 xxhash-3.4.1
 evehom  (e) reinvent4   main  …  CompChem  Python  REINVENT4  pip install --no-deps .
Processing /home/evehom/Data/CompChem/Python/REINVENT4
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: reinvent
  Building wheel for reinvent (pyproject.toml) ... done
  Created wheel for reinvent: filename=reinvent-4.3.5-py3-none-any.whl size=4128163 sha256=b1bbc11532cfdd174f631eaebed6f72059b4077f6f5b2567b8a487aeb3583080
  Stored in directory: /tmp/pip-ephem-wheel-cache-4iykh83j/wheels/cb/91/83/309f807ecbc840691b0f33034cf5643c13931b6d1cdcce4630
Successfully built reinvent
Installing collected packages: reinvent
Successfully installed reinvent-4.3.5
 evehom  (e) reinvent4   main  …  CompChem  Python  REINVENT4  reinvent --help
Traceback (most recent call last):
  File "/home/evehom/miniconda3/envs/reinvent4/bin/reinvent", line 5, in <module>
    from reinvent.Reinvent import main
  File "/home/evehom/miniconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/__init__.py", line 9, in <module>
    from reinvent import models
  File "/home/evehom/miniconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/models/__init__.py", line 3, in <module>
    from .reinvent.models.model import Model as ReinventModel
  File "/home/evehom/miniconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/models/reinvent/models/model.py", line 11, in <module>
    import torch
  File "/home/evehom/miniconda3/envs/reinvent4/lib/python3.10/site-packages/torch/__init__.py", line 237, in <module>
    from torch._C import *  # noqa: F403
ImportError: libcudnn.so.8: cannot open shared object file: No such file or directory
halx commented 6 months ago

Many thanks for the detailled error report!

I assume /home/evehom/miniconda3/envs/reinvent4/lib/python3.10/site-packages/nvidia/cudnn/lib/libcudnn.so.8 does not exist? Your output suggests that you already have cuda packages (and others) installed in $HOME/.local/lib/python3.10/site-packages. Conda does not reinstall packages if they have already been installed in another conda environment.

It is unclear to me though why it detects that your packages are already in $HOME/.local but cannot find the libraries therein at runtime. This is your clue here. If you do not need the installation in $HOME/.local you could delete it (but chances are that some other software of your own rely on it) and reinstall torch in your environment. Another quick fix could be to set $LD_LIBRARY_PATH.

Some info also here: https://stackoverflow.com/questions/62352699/conda-uses-local-packages

Hope that helps, Hannes.

Evert-Homan commented 6 months ago

That certainly helped. I wiped $HOME/.local, and then reinstalled REINVENT4 from scratch. Now the reinvent --help command gives the desired output, so I assume the code is working as it should.

Many thanks for your swift support, much appreciated.

BW/Evert