Error installing openfold

[evancollins1]

Hi,

I am having issues installing openfold. I have followed the install instructions included on the README thus far. I think the error I am getting is arising due to CUDA issues. Nevertheless, I know I have CUDA installed, and when I run echo $CUDA_HOME, I get the expected output of /usr/local/cuda-11.7.

Any ideas? Thanks!

Here's the command:

I run this line:

pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307'

.... and this error is produced ....

Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com Collecting openfold@ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307 Cloning https://github.com/aqlaboratory/openfold.git (to revision 4b41059694619831a7db195b7e0988fc4ff3a307) to /tmp/pip-install-z21z2t3v/openfold_db4c1e3c8ea741658d8b4c1771d14981 Running command git clone --filter=blob:none --quiet https://github.com/aqlaboratory/openfold.git /tmp/pip-install-z21z2t3v/openfold_db4c1e3c8ea741658d8b4c1771d14981 Running command git rev-parse -q --verify 'sha^4b41059694619831a7db195b7e0988fc4ff3a307' Running command git fetch -q https://github.com/aqlaboratory/openfold.git 4b41059694619831a7db195b7e0988fc4ff3a307 Running command git checkout -q 4b41059694619831a7db195b7e0988fc4ff3a307 Resolved https://github.com/aqlaboratory/openfold.git to commit 4b41059694619831a7db195b7e0988fc4ff3a307 Preparing metadata (setup.py) ... done Building wheels for collected packages: openfold Building wheel for openfold (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [178 lines of output] No CUDA runtime is found, using CUDA_HOME='/usr/local/cuda-11.7' running bdist_wheel running build

(Additional file text)

_Warning: Package 'openfold.utils.kernel.csrc' is absent from the packages configuration. !!

          ********************************************************************************
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'openfold.utils.kernel.csrc' as an importable package[^1],
          but it is absent from setuptools' `packages` configuration.
  
          This leads to an ambiguous overall configuration. If you want to distribute this
          package, please make sure that 'openfold.utils.kernel.csrc' is explicitly added
          to the `packages` configuration field.
  
          Alternatively, you can also rely on setuptools' discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
  
          You can read more about "package discovery" on setuptools documentation page:
  
          - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
  
          If you don't want 'openfold.utils.kernel.csrc' to be distributed and are
          already explicitly excluding 'openfold.utils.kernel.csrc' via
          `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
          you can try to use `exclude_package_data`, or `include-package-data=False` in
          combination with a more fine grained `package-data` configuration.
  
          You can read more about "package data files" on setuptools documentation page:
  
          - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
  
  
          [^1]: For Python, any directory (with suitable naming) can be imported,
                even if it does not contain any `.py` files.
                On the other hand, currently there is no concept of package data
                directory, all directories are treated like packages.
          ********************************************************************************
  
  !!
    check.warn(importable)
  creating build/lib.linux-x86_64-cpython-39/openfold/utils/kernel/csrc
  copying openfold/utils/kernel/csrc/softmax_cuda.cpp -> build/lib.linux-x86_64-cpython-39/openfold/utils/kernel/csrc
  copying openfold/utils/kernel/csrc/compat.h -> build/lib.linux-x86_64-cpython-39/openfold/utils/kernel/csrc
  copying openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -> build/lib.linux-x86_64-cpython-39/openfold/utils/kernel/csrc
  running build_ext

(Additional file text)

TypeError: expected string or bytes-like object [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 Failed to build openfold ERROR: Could not build wheels for openfold, which is required to install pyproject.toml-based projects

[AndrewLisz]

I also met the same problem. Have u solved this problem now?

[Yang-Wang-2020]

same here

[JoshAmpofo]

same here, need it to be installed urgently on colab but sadly haven't figured a workaround