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Local installation help? #590

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immunoliver opened this issue Jul 20, 2023 · 4 comments
Closed

Local installation help? #590

immunoliver opened this issue Jul 20, 2023 · 4 comments

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@immunoliver
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immunoliver commented Jul 20, 2023 •
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Hello,

I'm trying to install ESMfold locally and am struggling. When I paste the following code into the terminal, I get an error message.

pip install "fair-esm[esmfold]"
pip install 'dllogger @ git+https://github.com/NVIDIA/dllogger.git'
pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307'

It seems that pip install "fair-esm[esmfold]" works, as does pip install 'dllogger @ git+https://github.com/NVIDIA/dllogger.git', but when I try to install openfold I get the error below:

rekgowr@CS00056653:/mnt/c/Users/rekgowr/Documents/Lab/Structural_Biology$ pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307'
Defaulting to user installation because normal site-packages is not writeable
Collecting openfold@ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307
Cloning https://github.com/aqlaboratory/openfold.git (to revision 4b41059694619831a7db195b7e0988fc4ff3a307) to /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695
Running command git clone --filter=blob:none --quiet https://github.com/aqlaboratory/openfold.git /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695
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
╰─> [289 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-310
creating build/lib.linux-x86_64-cpython-310/openfold
copying openfold/config.py -> build/lib.linux-x86_64-cpython-310/openfold
copying openfold/init.py -> build/lib.linux-x86_64-cpython-310/openfold
creating build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/templates.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/feature_pipeline.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/data_modules.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/errors.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/input_pipeline.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/parsers.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/data_pipeline.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/mmcif_parsing.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/data_transforms.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/init.py -> build/lib.linux-x86_64-cpython-310/openfold/data
creating build/lib.linux-x86_64-cpython-310/openfold/np
copying openfold/np/residue_constants.py -> build/lib.linux-x86_64-cpython-310/openfold/np
copying openfold/np/init.py -> build/lib.linux-x86_64-cpython-310/openfold/np
copying openfold/np/protein.py -> build/lib.linux-x86_64-cpython-310/openfold/np
creating build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/template.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/primitives.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/triangular_multiplicative_update.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/embedders.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/evoformer.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/outer_product_mean.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/structure_module.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/msa.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/model.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/triangular_attention.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/heads.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/torchscript.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/dropout.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/pair_transition.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/init.py -> build/lib.linux-x86_64-cpython-310/openfold/model
creating build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/superimposition.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/seed.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/tensor_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/lr_schedulers.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/argparse.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/rigid_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/loss.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/logger.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/trace_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/feats.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/callbacks.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/chunk_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/validation_metrics.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/init.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/checkpointing.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/suppress_output.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/import_weights.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/exponential_moving_average.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
creating build/lib.linux-x86_64-cpython-310/openfold/resources
copying openfold/resources/init.py -> build/lib.linux-x86_64-cpython-310/openfold/resources
creating build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/utils.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/kalign.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/hhblits.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/hhsearch.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/init.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/jackhmmer.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
creating build/lib.linux-x86_64-cpython-310/openfold/np/relax
copying openfold/np/relax/utils.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax
copying openfold/np/relax/relax.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax
copying openfold/np/relax/cleanup.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax
copying openfold/np/relax/amber_minimize.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax
copying openfold/np/relax/init.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax
creating build/lib.linux-x86_64-cpython-310/openfold/utils/kernel
copying openfold/utils/kernel/attention_core.py -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel
copying openfold/utils/kernel/init.py -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel
running egg_info
creating openfold.egg-info
writing openfold.egg-info/PKG-INFO
writing dependency_links to openfold.egg-info/dependency_links.txt
writing top-level names to openfold.egg-info/top_level.txt
writing manifest file 'openfold.egg-info/SOURCES.txt'
reading manifest file 'openfold.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'openfold.egg-info/SOURCES.txt'
/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/command/build_py.py:201: _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-310/openfold/utils/kernel/csrc
  copying openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel/csrc
  copying openfold/utils/kernel/csrc/compat.h -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel/csrc
  copying openfold/utils/kernel/csrc/softmax_cuda.cpp -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel/csrc
  running build_ext
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/utils/cpp_extension.py:388: UserWarning: The detected CUDA version (11.5) has a minor version mismatch with the version that was used to compile PyTorch (11.7). Most likely this shouldn't be a problem.
    warnings.warn(CUDA_MISMATCH_WARN.format(cuda_str_version, torch.version.cuda))
  building 'attn_core_inplace_cuda' extension
  creating /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/build/temp.linux-x86_64-cpython-310
  creating /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/build/temp.linux-x86_64-cpython-310/openfold
  creating /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/build/temp.linux-x86_64-cpython-310/openfold/utils
  creating /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/build/temp.linux-x86_64-cpython-310/openfold/utils/kernel
  creating /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/build/temp.linux-x86_64-cpython-310/openfold/utils/kernel/csrc
  Emitting ninja build file /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/build/temp.linux-x86_64-cpython-310/build.ninja...
  Compiling objects...
  Allowing ninja to set a default number of workers... (overridable by setting the environment variable MAX_JOBS=N)
  [1/2] c++ -MMD -MF /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/build/temp.linux-x86_64-cpython-310/openfold/utils/kernel/csrc/softmax_cuda.o.d -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/openfold/utils/kernel/csrc/ -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include/torch/csrc/api/include -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include/TH -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include/THC -I/usr/include/python3.10 -c -c /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/openfold/utils/kernel/csrc/softmax_cuda.cpp -o /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/build/temp.linux-x86_64-cpython-310/openfold/utils/kernel/csrc/softmax_cuda.o -O3 -DVERSION_GE_1_1 -DVERSION_GE_1_3 -DVERSION_GE_1_5 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=attn_core_inplace_cuda -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++17
  [2/2] /usr/bin/nvcc  -I/tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/openfold/utils/kernel/csrc/ -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include/torch/csrc/api/include -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include/TH -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include/THC -I/usr/include/python3.10 -c -c /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -o /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/build/temp.linux-x86_64-cpython-310/openfold/utils/kernel/csrc/softmax_cuda_kernel.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_BFLOAT16_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' -O3 --use_fast_math -DVERSION_GE_1_1 -DVERSION_GE_1_3 -DVERSION_GE_1_5 -std=c++14 -maxrregcount=50 -U__CUDA_NO_HALF_OPERATORS__ -U__CUDA_NO_HALF_CONVERSIONS__ --expt-relaxed-constexpr --expt-extended-lambda -gencode arch=compute_37,code=sm_37 -gencode arch=compute_61,code=sm_61 -gencode arch=compute_70,code=sm_70 -gencode arch=compute_80,code=sm_80 -gencode arch=compute_52,code=sm_52 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=attn_core_inplace_cuda -D_GLIBCXX_USE_CXX11_ABI=0
  FAILED: /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/build/temp.linux-x86_64-cpython-310/openfold/utils/kernel/csrc/softmax_cuda_kernel.o
  /usr/bin/nvcc  -I/tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/openfold/utils/kernel/csrc/ -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include/torch/csrc/api/include -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include/TH -I/home/rekgowr/.local/lib/python3.10/site-packages/torch/include/THC -I/usr/include/python3.10 -c -c /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -o /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/build/temp.linux-x86_64-cpython-310/openfold/utils/kernel/csrc/softmax_cuda_kernel.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_BFLOAT16_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' -O3 --use_fast_math -DVERSION_GE_1_1 -DVERSION_GE_1_3 -DVERSION_GE_1_5 -std=c++14 -maxrregcount=50 -U__CUDA_NO_HALF_OPERATORS__ -U__CUDA_NO_HALF_CONVERSIONS__ --expt-relaxed-constexpr --expt-extended-lambda -gencode arch=compute_37,code=sm_37 -gencode arch=compute_61,code=sm_61 -gencode arch=compute_70,code=sm_70 -gencode arch=compute_80,code=sm_80 -gencode arch=compute_52,code=sm_52 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=attn_core_inplace_cuda -D_GLIBCXX_USE_CXX11_ABI=0
  nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/util/irange.h(54): warning #186-D: pointless comparison of unsigned integer with zero
            detected during:
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator==(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=size_t, one_sided=false, <unnamed>=0]"
  (61): here
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator!=(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=size_t, one_sided=false, <unnamed>=0]"
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/core/TensorImpl.h(77): here

  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/util/irange.h(54): warning #186-D: pointless comparison of unsigned integer with zero
            detected during:
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator==(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=std::size_t, one_sided=true, <unnamed>=0]"
  (61): here
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator!=(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=std::size_t, one_sided=true, <unnamed>=0]"
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/ATen/core/qualified_name.h(73): here

  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/util/irange.h(54): warning #186-D: pointless comparison of unsigned integer with zero
            detected during:
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator==(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=size_t, one_sided=false, <unnamed>=0]"
  (61): here
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator!=(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=size_t, one_sided=false, <unnamed>=0]"
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/core/TensorImpl.h(77): here

  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/util/irange.h(54): warning #186-D: pointless comparison of unsigned integer with zero
            detected during:
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator==(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=std::size_t, one_sided=true, <unnamed>=0]"
  (61): here
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator!=(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=std::size_t, one_sided=true, <unnamed>=0]"
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/ATen/core/qualified_name.h(73): here

  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/util/irange.h(54): warning #186-D: pointless comparison of unsigned integer with zero
            detected during:
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator==(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=size_t, one_sided=false, <unnamed>=0]"
  (61): here
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator!=(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=size_t, one_sided=false, <unnamed>=0]"
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/core/TensorImpl.h(77): here

  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/util/irange.h(54): warning #186-D: pointless comparison of unsigned integer with zero
            detected during:
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator==(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=std::size_t, one_sided=true, <unnamed>=0]"
  (61): here
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator!=(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=std::size_t, one_sided=true, <unnamed>=0]"
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/ATen/core/qualified_name.h(73): here

  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/util/irange.h(54): warning #186-D: pointless comparison of unsigned integer with zero
            detected during:
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator==(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=size_t, one_sided=false, <unnamed>=0]"
  (61): here
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator!=(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=size_t, one_sided=false, <unnamed>=0]"
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/core/TensorImpl.h(77): here

  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/util/irange.h(54): warning #186-D: pointless comparison of unsigned integer with zero
            detected during:
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator==(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=std::size_t, one_sided=true, <unnamed>=0]"
  (61): here
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator!=(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=std::size_t, one_sided=true, <unnamed>=0]"
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/ATen/core/qualified_name.h(73): here

  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/util/irange.h(54): warning #186-D: pointless comparison of unsigned integer with zero
            detected during:
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator==(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=size_t, one_sided=false, <unnamed>=0]"
  (61): here
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator!=(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=size_t, one_sided=false, <unnamed>=0]"
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/core/TensorImpl.h(77): here

  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/c10/util/irange.h(54): warning #186-D: pointless comparison of unsigned integer with zero
            detected during:
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator==(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=std::size_t, one_sided=true, <unnamed>=0]"
  (61): here
              instantiation of "__nv_bool c10::detail::integer_iterator<I, one_sided, <unnamed>>::operator!=(const c10::detail::integer_iterator<I, one_sided, <unnamed>> &) const [with I=std::size_t, one_sided=true, <unnamed>=0]"
  /home/rekgowr/.local/lib/python3.10/site-packages/torch/include/ATen/core/qualified_name.h(73): here

  /usr/include/c++/11/bits/std_function.h:435:145: error: parameter packs not expanded with ‘...’:
    435 |         function(_Functor&& __f)
        |
                                                    ^
  /usr/include/c++/11/bits/std_function.h:435:145: note:         ‘_ArgTypes’
  /usr/include/c++/11/bits/std_function.h:530:146: error: parameter packs not expanded with ‘...’:
    530 |         operator=(_Functor&& __f)
        |
                                                     ^
  /usr/include/c++/11/bits/std_function.h:530:146: note:         ‘_ArgTypes’
  ninja: build stopped: subcommand failed.
  Traceback (most recent call last):
    File "/home/rekgowr/.local/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1893, in _run_ninja_build
      subprocess.run(
    File "/usr/lib/python3.10/subprocess.py", line 524, in run
      raise CalledProcessError(retcode, process.args,
  subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1.

  The above exception was the direct cause of the following exception:

  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695/setup.py", line 74, in <module>
      setup(
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/__init__.py", line 107, in setup
      return distutils.core.setup(**attrs)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
      return run_commands(dist)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
      dist.run_commands()
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
      self.run_command(cmd)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
      super().run_command(command)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/home/rekgowr/.local/lib/python3.10/site-packages/wheel/bdist_wheel.py", line 343, in run
      self.run_command("build")
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
      super().run_command(command)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 131, in run
      self.run_command(cmd_name)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
      self.distribution.run_command(command)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
      super().run_command(command)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 84, in run
      _build_ext.run(self)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
      self.build_extensions()
    File "/home/rekgowr/.local/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 843, in build_extensions
      build_ext.build_extensions(self)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions
      self._build_extensions_serial()
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial
      self.build_extension(ext)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 246, in build_extension
      _build_ext.build_extension(self, ext)
    File "/home/rekgowr/.local/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 548, in build_extension
      objects = self.compiler.compile(
    File "/home/rekgowr/.local/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 658, in unix_wrap_ninja_compile
      _write_ninja_file_and_compile_objects(
    File "/home/rekgowr/.local/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1574, in _write_ninja_file_and_compile_objects
      _run_ninja_build(
    File "/home/rekgowr/.local/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1909, in _run_ninja_build
      raise RuntimeError(message) from e
  RuntimeError: Error compiling objects for extension
  [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

I'm very new to this and have less than a month's experience using the terminal - I appreciate that this is likely a simple problem. I have been able to troubleshoot everything else I've done so far using ChatGPT and Github, but this seems like there's something going on within the code I'm importing from you guys and I can't tell what's not compatible at my end unfortunately.

Please advise?

Thanks!
@immunoliver immunoliver closed this as not planned Won't fix, can't repro, duplicate, stale Aug 14, 2023
@susiegriggo
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I'm having this same issue - any chance you ended up resolving it?

@Lsz-20
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Lsz-20 commented Oct 25, 2023

The same question

@Budjavac
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same error, could this please resolved?

@lm-jkominek
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The team was disbanded last year, so there's not gonna be any fixes, unless there's community efforts.

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@susiegriggo @Lsz-20 @Budjavac @lm-jkominek @immunoliver