Dependency Conflict Issues with fsspec and scipy during PoseBench Environment Setup

[njujiangjk]

I'm encountering dependency resolution errors when trying to set up the PoseBench environment using
mamba env create -f environments/posebench_environment.yaml on Ubuntu 22.04.
FIRST ERROR:
ERROR: Cannot install -r /srv/seafile-data/Seafile/mycode/utils/PoseBench/environments/mambafnr16zwdmmh (line 33), -r /srv/seafile-data/Seafile/mycode/utils/PoseBench/environments/mambafnr16zwdmmh (line 50), -r /srv/seafile-data/Seafile/mycode/utils/PoseBench/environments/mambafnr16zwdmmh (line 56), -r /srv/seafile-data/Seafile/mycode/utils/PoseBench/environments/mambafnr16zwdmmh (line 73), -r /srv/seafile-data/Seafile/mycode/utils/PoseBench/environments/mambafnr16zwdmmh (line 88) and scipy==1.9.1because these package versions have conflicting dependencies.
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
critical libmamba pip failed to install packages
SECOND ERROR:
similar scipy conflict after removing fsspec==2025.7.0 version constraint
THIRD ERROR:
I modify yaml like scipy==1.9.1-->scipy and fsspec==2025.7.0-->fsspec
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
critical libmamba pip failed to install packages

THANK YOU !

[amorehead]

Hi, @njujiangjk.

Thanks for your interest! May I ask you to paste the full (third) error with its stacktrace? I can't tell what caused it from your initial description.

In the meantime, one idea that comes to mind would be removing fsspec from the YAML entirely, since I believe other dependencies require it already (and if not, then it should be removed).

[njujiangjk]

I extracted the pip section from the YAML file and tried to install using pip install. The error is as follows:
INFO: pip is looking at multiple versions of lightning to determine which version is compatible with other requirements. This could take a while.
ERROR: Cannot install -r environments/posebench_pip.txt (line 33), -r environments/posebench_pip.txt (line 49), -r environments/posebench_pip.txt (line 55), -r environments/posebench_pip.txt (line 72), -r environments/posebench_pip.txt (line 87) and fsspec==2025.7.0 because these package versions have conflicting dependencies.

The conflict is caused by:
The user requested fsspec==2025.7.0
datamol 0.12.4 depends on fsspec>=2021.9
fastparquet 2024.11.0 depends on fsspec
gcsfs 2025.7.0 depends on fsspec==2025.7.0
huggingface-hub 0.19.4 depends on fsspec>=2023.5.0
lightning 2.1.3 depends on fsspec<2025.0 and >=2022.5.0

To fix this you could try to:

1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts

[amorehead]

In that case, the solution will be to upgrade the version of lightning. You can either drop the version number of lightning, or you can likely install the latest version of 2.5.6. Let me know if this fixes the issue, and if so, I will update the main branch accordingly.

[njujiangjk]

So I drop the vision number of lightning, but:
The conflict is caused by:
The user requested rdkit
datamol 0.12.4 depends on rdkit
pdbeccdutils 0.8.6 depends on rdkit==2023.9.6
plinder 0.2.25.dev9+gb01598b depends on rdkit>=2024.03.6

[amorehead]

Hi, @njujiangjk.

Apologies for the repeated back-and-forth debugging of this issue. I currently don't have easy access to a machine to test this Linux dependency issue directly, but we should be able to figure it out. It looks like the error above can be fixed by upgrading pdbeccdutils to version 1.0.0 which allows rdkit>=2023.9.6.

[amorehead]

Hi, @njujiangjk. Did this resolve the issue for you?

[njujiangjk]

sorry, I install the git+ packages
git+https://github.com/NVIDIA/dllogger.git@v1.0.0
git+https://github.com/amorehead/Meeko.git@patch-1
git+https://github.com/amorehead/openfold.git@4ef71646ed031f69716097a9352d21778369136d
git+https://github.com/amorehead/plinder.git@posebench
git+https://github.com/amorehead/posebusters.git@posebench-0.7.0
git+https://github.com/amorehead/posecheck.git@posebench
git+https://github.com/amorehead/ProLIF.git@patch-2

ERROR:
self.build_extensions()

    File "/home/nju-jump/anaconda3/envs/PoseBench/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 522, in build_extensions

      _check_cuda_version(compiler_name, compiler_version)

    File "/home/nju-jump/anaconda3/envs/PoseBench/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 417, in _check_cuda_version

      raise RuntimeError(CUDA_MISMATCH_MESSAGE.format(cuda_str_version, torch.version.cuda))

  RuntimeError:

  The detected CUDA version (12.4) mismatches the version that was used to compile

  PyTorch (11.8). Please make sure to use the same CUDA versions.

  

  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

ERROR: Failed building wheel for openfold

Running setup.py clean for openfold

Building wheel for plinder (pyproject.toml) ... done

Created wheel for plinder: filename=plinder-0.2.25.dev9+gb01598b-py3-none-any.whl size=5011015 sha256=226d71196ff320a9a49a0341e1d008fee9db2c939c22861ec111f10a54ad2591

Stored in directory: /tmp/pip-ephem-wheel-cache-3_t6xb0t/wheels/de/de/18/f025464004f30aefddef7cc9b516fda130d294acd1eeabfeba

Building wheel for posebusters (pyproject.toml) ... done

Created wheel for posebusters: filename=posebusters-0.4.5-py3-none-any.whl size=556380 sha256=7a13f6b41134f6b8a36d751c302cc55f0063e680d07d7a052e3d99195a127fa3

Stored in directory: /tmp/pip-ephem-wheel-cache-3_t6xb0t/wheels/92/26/53/77a27ff2e445edd898555ba4a34120b898f7dfcde0a8eb3f11

Building wheel for posecheck (setup.py) ... done

Created wheel for posecheck: filename=posecheck-1.1-py3-none-any.whl size=24172 sha256=91b53ec3e493f6823cfe791425f139d557a25a882787a7c1eef9b7f5d8b2a4ed

Stored in directory: /tmp/pip-ephem-wheel-cache-3_t6xb0t/wheels/6d/c3/76/cd093dfbd2078f7c76f0ce789f469e6cbf9c36288805d31f41

Building wheel for prolif (pyproject.toml) ... done

Created wheel for prolif: filename=prolif-2.0.3-py3-none-any.whl size=5146547 sha256=730ba60766c9664838bef6c4bb81bc359c6500aee67dd85d11009fb81d5104dc

Stored in directory: /tmp/pip-ephem-wheel-cache-3_t6xb0t/wheels/28/f4/19/2784b9f65b8015e7b649adfa4cc5157d2f4e974dc225a32bfd

Building wheel for timeout_decorator (setup.py) ... done

Created wheel for timeout_decorator: filename=timeout_decorator-0.5.0-py3-none-any.whl size=5006 sha256=92bd83b89220e283ed84badc7eaf7846e8f839a6646ceebad241f3d947f5eb0d

Stored in directory: /home/nju-jump/.cache/pip/wheels/b3/4c/b8/3fb8e41b4c41eeb41bb7db3ac35d58cd03229434d9ceb52ac3

Successfully built DLLogger meeko plinder posebusters posecheck prolif timeout_decorator

Failed to build openfold

ERROR: Could not build wheels for openfold, which is required to install pyproject.toml-based projects

maybe my cuda version is 12.4 not 11.7 cause it ,so I am trying to create environment with cuda12

[amorehead]

Hi, @njujiangjk.

Yes, I developed this package for CUDA 11, so 12 may not work out of the box.

[njujiangjk]

thank you!

[amorehead]

Are you now able to build the package successfully?