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facebookresearch / esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins
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openfold installation #456

Open saeid976 opened 1 year ago

saeid976 commented 1 year ago

hi dear support team

i try to install openfold for loading ESMFold, but error in below occured: use this command: pip install git+https://github.com/aqlaboratory/openfold.git@6908936b68ae89f67755240e2f588c09ec31d4c8

error: Collecting git+https://github.com/aqlaboratory/openfold.git@6908936b68ae89f67755240e2f588c09ec31d4c8 Cloning https://github.com/aqlaboratory/openfold.git (to revision 6908936b68ae89f67755240e2f588c09ec31d4c8) to /tmp/pip-req-build-7tcd44wx Running command git clone --quiet https://github.com/aqlaboratory/openfold.git /tmp/pip-req-build-7tcd44wx Running command git rev-parse -q --verify 'sha^6908936b68ae89f67755240e2f588c09ec31d4c8' Running command git fetch -q https://github.com/aqlaboratory/openfold.git 6908936b68ae89f67755240e2f588c09ec31d4c8 fatal: Couldn't find remote ref 6908936b68ae89f67755240e2f588c09ec31d4c8 Unexpected end of command stream error: subprocess-exited-with-error

× git fetch -q https://github.com/aqlaboratory/openfold.git 6908936b68ae89f67755240e2f588c09ec31d4c8 did not run successfully. │ exit code: 128 ╰─> See above for output.

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

× git fetch -q https://github.com/aqlaboratory/openfold.git 6908936b68ae89f67755240e2f588c09ec31d4c8 did not run successfully. │ exit code: 128 ╰─> See above for output.

how can i fixed this error?

Thanks

linda5mith commented 1 year ago

I am also having trouble installing openfold. 

pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307'
Collecting openfold@ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307
  Cloning https://github.com/aqlaboratory/openfold.git (to revision 4b41059694619831a7db195b7e0988fc4ff3a307) to /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22
  Running command git clone --filter=blob:none --quiet https://github.com/aqlaboratory/openfold.git /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22
  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
  ╰─> [176 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-3.7
      creating build/lib.linux-x86_64-3.7/openfold
      copying openfold/__init__.py -> build/lib.linux-x86_64-3.7/openfold
      copying openfold/config.py -> build/lib.linux-x86_64-3.7/openfold
      creating build/lib.linux-x86_64-3.7/openfold/resources
      copying openfold/resources/__init__.py -> build/lib.linux-x86_64-3.7/openfold/resources
      creating build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/input_pipeline.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/data_transforms.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/data_pipeline.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/parsers.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/data_modules.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/__init__.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/templates.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/mmcif_parsing.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/errors.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/feature_pipeline.py -> build/lib.linux-x86_64-3.7/openfold/data
      creating build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/loss.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/rigid_utils.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/logger.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/checkpointing.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/trace_utils.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/lr_schedulers.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/__init__.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/feats.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/exponential_moving_average.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/seed.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/suppress_output.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/chunk_utils.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/superimposition.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/validation_metrics.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/import_weights.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/tensor_utils.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/callbacks.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/argparse.py -> build/lib.linux-x86_64-3.7/openfold/utils
      creating build/lib.linux-x86_64-3.7/openfold/np
      copying openfold/np/residue_constants.py -> build/lib.linux-x86_64-3.7/openfold/np
      copying openfold/np/__init__.py -> build/lib.linux-x86_64-3.7/openfold/np
      copying openfold/np/protein.py -> build/lib.linux-x86_64-3.7/openfold/np
      creating build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/pair_transition.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/template.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/torchscript.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/outer_product_mean.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/structure_module.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/__init__.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/evoformer.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/triangular_multiplicative_update.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/embedders.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/msa.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/triangular_attention.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/model.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/primitives.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/dropout.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/heads.py -> build/lib.linux-x86_64-3.7/openfold/model
      creating build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/utils.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/jackhmmer.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/__init__.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/kalign.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/hhblits.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/hhsearch.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      creating build/lib.linux-x86_64-3.7/openfold/utils/kernel
      copying openfold/utils/kernel/__init__.py -> build/lib.linux-x86_64-3.7/openfold/utils/kernel
      copying openfold/utils/kernel/attention_core.py -> build/lib.linux-x86_64-3.7/openfold/utils/kernel
      creating build/lib.linux-x86_64-3.7/openfold/np/relax
      copying openfold/np/relax/utils.py -> build/lib.linux-x86_64-3.7/openfold/np/relax
      copying openfold/np/relax/amber_minimize.py -> build/lib.linux-x86_64-3.7/openfold/np/relax
      copying openfold/np/relax/relax.py -> build/lib.linux-x86_64-3.7/openfold/np/relax
      copying openfold/np/relax/__init__.py -> build/lib.linux-x86_64-3.7/openfold/np/relax
      copying openfold/np/relax/cleanup.py -> build/lib.linux-x86_64-3.7/openfold/np/relax
      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'
      creating build/lib.linux-x86_64-3.7/openfold/utils/kernel/csrc
      copying openfold/utils/kernel/csrc/compat.h -> build/lib.linux-x86_64-3.7/openfold/utils/kernel/csrc
      copying openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -> build/lib.linux-x86_64-3.7/openfold/utils/kernel/csrc
      copying openfold/utils/kernel/csrc/softmax_cuda.cpp -> build/lib.linux-x86_64-3.7/openfold/utils/kernel/csrc
      running build_ext
      /home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py:813: UserWarning: The detected CUDA version (11.5) has a minor version mismatch with the version that was used to compile PyTorch (11.3). Most likely this shouldn't be a problem.
        warnings.warn(CUDA_MISMATCH_WARN.format(cuda_str_version, torch.version.cuda))
      /home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py:820: UserWarning: There are no g++ version bounds defined for CUDA version 11.5
        warnings.warn(f'There are no {compiler_name} version bounds defined for CUDA version {cuda_str_version}')
      building 'attn_core_inplace_cuda' extension
      creating /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7
      creating /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold
      creating /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold/utils
      creating /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold/utils/kernel
      creating /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold/utils/kernel/csrc
      Emitting ninja build file /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/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-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold/utils/kernel/csrc/softmax_cuda.o.d -pthread -B /home/linda/programs/anaconda3/envs/esmfold/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/ -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/TH -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/THC -I/home/linda/programs/anaconda3/envs/esmfold/include/python3.7m -c -c /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/softmax_cuda.cpp -o /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/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++14
      cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
      [2/2] /usr/bin/nvcc  -I/tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/ -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/TH -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/THC -I/home/linda/programs/anaconda3/envs/esmfold/include/python3.7m -c -c /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -o /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/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_75,code=sm_75 -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-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold/utils/kernel/csrc/softmax_cuda_kernel.o
      /usr/bin/nvcc  -I/tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/ -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/TH -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/THC -I/home/linda/programs/anaconda3/envs/esmfold/include/python3.7m -c -c /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -o /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/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_75,code=sm_75 -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
      /home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/c10/core/SymInt.h(84): warning #68-D: integer conversion resulted in a change of sign

      /home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/c10/core/SymInt.h(84): warning #68-D: integer conversion resulted in a change of sign

      /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/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 1814, in _run_ninja_build
          env=env)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/subprocess.py", line 512, in run
          output=stdout, stderr=stderr)
      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 36, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/setup.py", line 113, in <module>
          'Programming Language :: Python :: 3.7,'
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/setuptools/__init__.py", line 153, in setup
          return distutils.core.setup(**attrs)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/core.py", line 148, in setup
          dist.run_commands()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/dist.py", line 966, in run_commands
          self.run_command(cmd)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/dist.py", line 985, in run_command
          cmd_obj.run()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 325, in run
          self.run_command("build")
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/cmd.py", line 313, in run_command
          self.distribution.run_command(command)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/dist.py", line 985, in run_command
          cmd_obj.run()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/command/build.py", line 135, in run
          self.run_command(cmd_name)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/cmd.py", line 313, in run_command
          self.distribution.run_command(command)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/dist.py", line 985, in run_command
          cmd_obj.run()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/setuptools/command/build_ext.py", line 79, in run
          _build_ext.run(self)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/command/build_ext.py", line 340, in run
          self.build_extensions()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 765, in build_extensions
          build_ext.build_extensions(self)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/command/build_ext.py", line 449, in build_extensions
          self._build_extensions_serial()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/command/build_ext.py", line 474, in _build_extensions_serial
          self.build_extension(ext)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/setuptools/command/build_ext.py", line 202, in build_extension
          _build_ext.build_extension(self, ext)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/command/build_ext.py", line 534, in build_extension
          depends=ext.depends)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 595, in unix_wrap_ninja_compile
          with_cuda=with_cuda)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 1492, in _write_ninja_file_and_compile_objects
          error_prefix='Error compiling objects for extension')
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 1824, 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
Installing collected packages: openfold
  Running setup.py install for openfold ... error
  error: subprocess-exited-with-error

  × Running setup.py install for openfold did not run successfully.
  │ exit code: 1
  ╰─> [178 lines of output]
      running install
      /home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
        setuptools.SetuptoolsDeprecationWarning,
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-3.7
      creating build/lib.linux-x86_64-3.7/openfold
      copying openfold/__init__.py -> build/lib.linux-x86_64-3.7/openfold
      copying openfold/config.py -> build/lib.linux-x86_64-3.7/openfold
      creating build/lib.linux-x86_64-3.7/openfold/resources
      copying openfold/resources/__init__.py -> build/lib.linux-x86_64-3.7/openfold/resources
      creating build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/input_pipeline.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/data_transforms.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/data_pipeline.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/parsers.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/data_modules.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/__init__.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/templates.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/mmcif_parsing.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/errors.py -> build/lib.linux-x86_64-3.7/openfold/data
      copying openfold/data/feature_pipeline.py -> build/lib.linux-x86_64-3.7/openfold/data
      creating build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/loss.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/rigid_utils.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/logger.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/checkpointing.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/trace_utils.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/lr_schedulers.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/__init__.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/feats.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/exponential_moving_average.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/seed.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/suppress_output.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/chunk_utils.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/superimposition.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/validation_metrics.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/import_weights.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/tensor_utils.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/callbacks.py -> build/lib.linux-x86_64-3.7/openfold/utils
      copying openfold/utils/argparse.py -> build/lib.linux-x86_64-3.7/openfold/utils
      creating build/lib.linux-x86_64-3.7/openfold/np
      copying openfold/np/residue_constants.py -> build/lib.linux-x86_64-3.7/openfold/np
      copying openfold/np/__init__.py -> build/lib.linux-x86_64-3.7/openfold/np
      copying openfold/np/protein.py -> build/lib.linux-x86_64-3.7/openfold/np
      creating build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/pair_transition.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/template.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/torchscript.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/outer_product_mean.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/structure_module.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/__init__.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/evoformer.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/triangular_multiplicative_update.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/embedders.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/msa.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/triangular_attention.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/model.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/primitives.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/dropout.py -> build/lib.linux-x86_64-3.7/openfold/model
      copying openfold/model/heads.py -> build/lib.linux-x86_64-3.7/openfold/model
      creating build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/utils.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/jackhmmer.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/__init__.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/kalign.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/hhblits.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      copying openfold/data/tools/hhsearch.py -> build/lib.linux-x86_64-3.7/openfold/data/tools
      creating build/lib.linux-x86_64-3.7/openfold/utils/kernel
      copying openfold/utils/kernel/__init__.py -> build/lib.linux-x86_64-3.7/openfold/utils/kernel
      copying openfold/utils/kernel/attention_core.py -> build/lib.linux-x86_64-3.7/openfold/utils/kernel
      creating build/lib.linux-x86_64-3.7/openfold/np/relax
      copying openfold/np/relax/utils.py -> build/lib.linux-x86_64-3.7/openfold/np/relax
      copying openfold/np/relax/amber_minimize.py -> build/lib.linux-x86_64-3.7/openfold/np/relax
      copying openfold/np/relax/relax.py -> build/lib.linux-x86_64-3.7/openfold/np/relax
      copying openfold/np/relax/__init__.py -> build/lib.linux-x86_64-3.7/openfold/np/relax
      copying openfold/np/relax/cleanup.py -> build/lib.linux-x86_64-3.7/openfold/np/relax
      running 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
      reading manifest file 'openfold.egg-info/SOURCES.txt'
      adding license file 'LICENSE'
      writing manifest file 'openfold.egg-info/SOURCES.txt'
      creating build/lib.linux-x86_64-3.7/openfold/utils/kernel/csrc
      copying openfold/utils/kernel/csrc/compat.h -> build/lib.linux-x86_64-3.7/openfold/utils/kernel/csrc
      copying openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -> build/lib.linux-x86_64-3.7/openfold/utils/kernel/csrc
      copying openfold/utils/kernel/csrc/softmax_cuda.cpp -> build/lib.linux-x86_64-3.7/openfold/utils/kernel/csrc
      running build_ext
      /home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py:813: UserWarning: The detected CUDA version (11.5) has a minor version mismatch with the version that was used to compile PyTorch (11.3). Most likely this shouldn't be a problem.
        warnings.warn(CUDA_MISMATCH_WARN.format(cuda_str_version, torch.version.cuda))
      /home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py:820: UserWarning: There are no g++ version bounds defined for CUDA version 11.5
        warnings.warn(f'There are no {compiler_name} version bounds defined for CUDA version {cuda_str_version}')
      building 'attn_core_inplace_cuda' extension
      creating /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7
      creating /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold
      creating /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold/utils
      creating /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold/utils/kernel
      creating /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold/utils/kernel/csrc
      Emitting ninja build file /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/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-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold/utils/kernel/csrc/softmax_cuda.o.d -pthread -B /home/linda/programs/anaconda3/envs/esmfold/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/ -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/TH -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/THC -I/home/linda/programs/anaconda3/envs/esmfold/include/python3.7m -c -c /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/softmax_cuda.cpp -o /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/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++14
      cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
      [2/2] /usr/bin/nvcc  -I/tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/ -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/TH -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/THC -I/home/linda/programs/anaconda3/envs/esmfold/include/python3.7m -c -c /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -o /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/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_75,code=sm_75 -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-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/openfold/utils/kernel/csrc/softmax_cuda_kernel.o
      /usr/bin/nvcc  -I/tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/ -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/TH -I/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/THC -I/home/linda/programs/anaconda3/envs/esmfold/include/python3.7m -c -c /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -o /tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/build/temp.linux-x86_64-3.7/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_75,code=sm_75 -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
      /home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/c10/core/SymInt.h(84): warning #68-D: integer conversion resulted in a change of sign

      /home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/include/c10/core/SymInt.h(84): warning #68-D: integer conversion resulted in a change of sign

      /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/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 1814, in _run_ninja_build
          env=env)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/subprocess.py", line 512, in run
          output=stdout, stderr=stderr)
      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 36, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-fgp2ugry/openfold_f5409cc00d3447f0879c2d2273e84b22/setup.py", line 113, in <module>
          'Programming Language :: Python :: 3.7,'
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/setuptools/__init__.py", line 153, in setup
          return distutils.core.setup(**attrs)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/core.py", line 148, in setup
          dist.run_commands()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/dist.py", line 966, in run_commands
          self.run_command(cmd)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/dist.py", line 985, in run_command
          cmd_obj.run()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/setuptools/command/install.py", line 68, in run
          return orig.install.run(self)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/command/install.py", line 545, in run
          self.run_command('build')
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/cmd.py", line 313, in run_command
          self.distribution.run_command(command)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/dist.py", line 985, in run_command
          cmd_obj.run()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/command/build.py", line 135, in run
          self.run_command(cmd_name)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/cmd.py", line 313, in run_command
          self.distribution.run_command(command)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/dist.py", line 985, in run_command
          cmd_obj.run()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/setuptools/command/build_ext.py", line 79, in run
          _build_ext.run(self)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/command/build_ext.py", line 340, in run
          self.build_extensions()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 765, in build_extensions
          build_ext.build_extensions(self)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/command/build_ext.py", line 449, in build_extensions
          self._build_extensions_serial()
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/command/build_ext.py", line 474, in _build_extensions_serial
          self.build_extension(ext)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/setuptools/command/build_ext.py", line 202, in build_extension
          _build_ext.build_extension(self, ext)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/distutils/command/build_ext.py", line 534, in build_extension
          depends=ext.depends)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 595, in unix_wrap_ninja_compile
          with_cuda=with_cuda)
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 1492, in _write_ninja_file_and_compile_objects
          error_prefix='Error compiling objects for extension')
        File "/home/linda/programs/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 1824, 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: legacy-install-failure

× Encountered error while trying to install package.
╰─> openfold

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

Please advise! Thank you!

johnnytam100 commented 1 year ago

same issue.

nikita-smetanin commented 1 year ago

Hi @saeid976 please use openfold revision 4b41059694619831a7db195b7e0988fc4ff3a307 as in the readme https://github.com/facebookresearch/esm/blob/main/README.md#getting-started-with-this-repo-

@linda5mith The error looks like an odd nvcc version or something similar, please tell what's your nvcc --version is.

Paulie-ai commented 1 year ago

when i install esmfold by conda and yml file, i meet the trouble with : when i import torch, its show as Traceback (most recent call last): File "", line 1, in File "/home/anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/init.py", line 202, in from torch._C import * # noqa: F403 ImportError: /home//anaconda3/envs/esmfold/lib/python3.7/site-packages/torch/lib/libtorch_cuda_cpp.so: invalid ELF header

Artemisimetra commented 1 year ago

@nikitos9000 I am getting the same issue during installation as saeid976.

Is esm compatible with Pytorch 2.0.0?

yuanqm55 commented 1 year ago

same issue. I can't install openfold via pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307'

Paulie-ai commented 1 year ago

same issue. I can't install openfold via pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307'

maybe not correct python version or something with your network, i try later and fixed this errors. Hope help.

pjsample commented 1 year ago

I encountered this error when attempting a fresh install of ESMFold. I referenced the Pytorch version of a previously installed working version which was 1.13.1. Installing that version corrected the issue with Openfold.

pip install torch==1.13.1

However, I am now running into this error when trying to run esm.pretrained.esmfold_v1().

ImportError: cannot import name 'seed_everything' from 'pytorch_lightning.utilities.seed'

Which I believe is another version incompatibility issue.

Update: Yes, changing the Pytorch Lightning version to 1.9 fixed it. pip install pytorch-lightning==1.9.0

Paulie-ai commented 1 year ago

@yuanqm55 this issue can be settle by git clone openfold rep directly, with python setup.py install, it always need correct CUDA envs

Amelie-Schreiber commented 1 year ago

@Paulie-ai could you say more and maybe provide more details? I'm encountering this also when trying to use the protein programming language as well.

Paulie-ai commented 1 year ago

@Paulie-ai could you say more and maybe provide more details? I'm encountering this also when trying to use the protein programming language as well.

@Paulie-ai could you say more and maybe provide more details? I'm encountering this also when trying to use the protein programming language as well.

it can be solve just manual installation openfold, hope this help