Comments (4)
Moricant
commented on September 28, 2024
Full error output from first attempt:
Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cu117
Looking in links: https://pytorch-geometric.com/whl/torch-1.13.1+cu117.html
Collecting git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307
Cloning https://github.com/aqlaboratory/openfold.git (to revision 4b41059694619831a7db195b7e0988fc4ff3a307) to /tmp/pip-req-build-f4m3pp8g
Running command git clone --filter=blob:none --quiet https://github.com/aqlaboratory/openfold.git /tmp/pip-req-build-f4m3pp8g
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
╰─> [212 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-39
creating build/lib.linux-x86_64-cpython-39/openfold
copying openfold/config.py -> build/lib.linux-x86_64-cpython-39/openfold
copying openfold/init.py -> build/lib.linux-x86_64-cpython-39/openfold
creating build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/outer_product_mean.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/dropout.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/triangular_attention.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/torchscript.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/primitives.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/model.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/evoformer.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/triangular_multiplicative_update.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/structure_module.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/msa.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/template.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/pair_transition.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/heads.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/init.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/embedders.py -> build/lib.linux-x86_64-cpython-39/openfold/model
creating build/lib.linux-x86_64-cpython-39/openfold/resources
copying openfold/resources/init.py -> build/lib.linux-x86_64-cpython-39/openfold/resources
creating build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/parsers.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/errors.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/data_transforms.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/input_pipeline.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/mmcif_parsing.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/data_modules.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/templates.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/feature_pipeline.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/data_pipeline.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/init.py -> build/lib.linux-x86_64-cpython-39/openfold/data
creating build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/tensor_utils.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/logger.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/chunk_utils.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/loss.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/argparse.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/exponential_moving_average.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/suppress_output.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/validation_metrics.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/callbacks.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/superimposition.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/trace_utils.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/import_weights.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/feats.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/seed.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/checkpointing.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/rigid_utils.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/init.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/lr_schedulers.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
creating build/lib.linux-x86_64-cpython-39/openfold/np
copying openfold/np/protein.py -> build/lib.linux-x86_64-cpython-39/openfold/np
copying openfold/np/residue_constants.py -> build/lib.linux-x86_64-cpython-39/openfold/np
copying openfold/np/init.py -> build/lib.linux-x86_64-cpython-39/openfold/np
creating build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/hhsearch.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/utils.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/kalign.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/hhblits.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/jackhmmer.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/init.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
creating build/lib.linux-x86_64-cpython-39/openfold/utils/kernel
copying openfold/utils/kernel/attention_core.py -> build/lib.linux-x86_64-cpython-39/openfold/utils/kernel
copying openfold/utils/kernel/init.py -> build/lib.linux-x86_64-cpython-39/openfold/utils/kernel
creating build/lib.linux-x86_64-cpython-39/openfold/np/relax
copying openfold/np/relax/amber_minimize.py -> build/lib.linux-x86_64-cpython-39/openfold/np/relax
copying openfold/np/relax/utils.py -> build/lib.linux-x86_64-cpython-39/openfold/np/relax
copying openfold/np/relax/cleanup.py -> build/lib.linux-x86_64-cpython-39/openfold/np/relax
copying openfold/np/relax/relax.py -> build/lib.linux-x86_64-cpython-39/openfold/np/relax
copying openfold/np/relax/init.py -> build/lib.linux-x86_64-cpython-39/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'
/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _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_kernel.cu -> 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.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.cpp -> 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
building 'attn_core_inplace_cuda' extension
creating /tmp/pip-req-build-f4m3pp8g/build/temp.linux-x86_64-cpython-39
creating /tmp/pip-req-build-f4m3pp8g/build/temp.linux-x86_64-cpython-39/openfold
creating /tmp/pip-req-build-f4m3pp8g/build/temp.linux-x86_64-cpython-39/openfold/utils
creating /tmp/pip-req-build-f4m3pp8g/build/temp.linux-x86_64-cpython-39/openfold/utils/kernel
creating /tmp/pip-req-build-f4m3pp8g/build/temp.linux-x86_64-cpython-39/openfold/utils/kernel/csrc
Emitting ninja build file /tmp/pip-req-build-f4m3pp8g/build/temp.linux-x86_64-cpython-39/build.ninja...
Compiling objects...
Allowing ninja to set a default number of workers... (overridable by setting the environment variable MAX_JOBS=N)
[1/2] /home/apps/anaconda3/envs/diffdock/bin/nvcc -I/tmp/pip-req-build-f4m3pp8g/openfold/utils/kernel/csrc/ -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include/TH -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include/THC -I/home/apps/anaconda3/envs/diffdock/include -I/home/apps/anaconda3/envs/diffdock/include/python3.9 -c -c /tmp/pip-req-build-f4m3pp8g/openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -o /tmp/pip-req-build-f4m3pp8g/build/temp.linux-x86_64-cpython-39/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_89,code=sm_89 -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-req-build-f4m3pp8g/build/temp.linux-x86_64-cpython-39/openfold/utils/kernel/csrc/softmax_cuda_kernel.o
/home/apps/anaconda3/envs/diffdock/bin/nvcc -I/tmp/pip-req-build-f4m3pp8g/openfold/utils/kernel/csrc/ -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include/TH -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include/THC -I/home/apps/anaconda3/envs/diffdock/include -I/home/apps/anaconda3/envs/diffdock/include/python3.9 -c -c /tmp/pip-req-build-f4m3pp8g/openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -o /tmp/pip-req-build-f4m3pp8g/build/temp.linux-x86_64-cpython-39/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_89,code=sm_89 -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 fatal : Unsupported gpu architecture 'compute_89'
[2/2] c++ -MMD -MF /tmp/pip-req-build-f4m3pp8g/build/temp.linux-x86_64-cpython-39/openfold/utils/kernel/csrc/softmax_cuda.o.d -pthread -B /home/apps/anaconda3/envs/diffdock/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/apps/anaconda3/envs/diffdock/include -fPIC -O2 -isystem /home/apps/anaconda3/envs/diffdock/include -fPIC -I/tmp/pip-req-build-f4m3pp8g/openfold/utils/kernel/csrc/ -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include/TH -I/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/include/THC -I/home/apps/anaconda3/envs/diffdock/include -I/home/apps/anaconda3/envs/diffdock/include/python3.9 -c -c /tmp/pip-req-build-f4m3pp8g/openfold/utils/kernel/csrc/softmax_cuda.cpp -o /tmp/pip-req-build-f4m3pp8g/build/temp.linux-x86_64-cpython-39/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
ninja: build stopped: subcommand failed.
Traceback (most recent call last):
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/utils/cpp_extension.py", line 1900, in _run_ninja_build
subprocess.run(
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/subprocess.py", line 528, 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-req-build-f4m3pp8g/setup.py", line 74, in <module>
setup(
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/__init__.py", line 104, in setup
return distutils.core.setup(**attrs)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 184, in setup
return run_commands(dist)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 200, in run_commands
dist.run_commands()
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/dist.py", line 967, in run_command
super().run_command(command)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 368, in run
self.run_command("build")
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/dist.py", line 967, in run_command
super().run_command(command)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 132, in run
self.run_command(cmd_name)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/dist.py", line 967, in run_command
super().run_command(command)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/command/build_ext.py", line 91, in run
_build_ext.run(self)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 359, in run
self.build_extensions()
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/utils/cpp_extension.py", line 843, in build_extensions
build_ext.build_extensions(self)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 479, in build_extensions
self._build_extensions_serial()
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 505, in _build_extensions_serial
self.build_extension(ext)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/command/build_ext.py", line 252, in build_extension
_build_ext.build_extension(self, ext)
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 560, in build_extension
objects = self.compiler.compile(
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/utils/cpp_extension.py", line 658, in unix_wrap_ninja_compile
_write_ninja_file_and_compile_objects(
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/utils/cpp_extension.py", line 1573, in _write_ninja_file_and_compile_objects
_run_ninja_build(
File "/home/apps/anaconda3/envs/diffdock/lib/python3.9/site-packages/torch/utils/cpp_extension.py", line 1916, 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
from diffdock.
Moricant
commented on September 28, 2024
Full output from second attempt:
Collecting openfold@ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307
Cloning https://github.com/aqlaboratory/openfold.git (to revision 4b41059694619831a7db195b7e0988fc4ff3a307) to /tmp/pip-install-jbp541x2/openfold_505a5225e2ba4112a59f2eb35c36361c
Running command git clone --filter=blob:none --quiet https://github.com/aqlaboratory/openfold.git /tmp/pip-install-jbp541x2/openfold_505a5225e2ba4112a59f2eb35c36361c
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
╰─> [179 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-39
creating build/lib.linux-x86_64-cpython-39/openfold
copying openfold/config.py -> build/lib.linux-x86_64-cpython-39/openfold
copying openfold/init.py -> build/lib.linux-x86_64-cpython-39/openfold
creating build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/outer_product_mean.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/dropout.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/triangular_attention.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/torchscript.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/primitives.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/model.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/evoformer.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/triangular_multiplicative_update.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/structure_module.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/msa.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/template.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/pair_transition.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/heads.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/init.py -> build/lib.linux-x86_64-cpython-39/openfold/model
copying openfold/model/embedders.py -> build/lib.linux-x86_64-cpython-39/openfold/model
creating build/lib.linux-x86_64-cpython-39/openfold/resources
copying openfold/resources/init.py -> build/lib.linux-x86_64-cpython-39/openfold/resources
creating build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/parsers.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/errors.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/data_transforms.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/input_pipeline.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/mmcif_parsing.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/data_modules.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/templates.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/feature_pipeline.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/data_pipeline.py -> build/lib.linux-x86_64-cpython-39/openfold/data
copying openfold/data/init.py -> build/lib.linux-x86_64-cpython-39/openfold/data
creating build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/tensor_utils.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/logger.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/chunk_utils.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/loss.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/argparse.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/exponential_moving_average.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/suppress_output.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/validation_metrics.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/callbacks.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/superimposition.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/trace_utils.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/import_weights.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/feats.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/seed.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/checkpointing.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/rigid_utils.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/init.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
copying openfold/utils/lr_schedulers.py -> build/lib.linux-x86_64-cpython-39/openfold/utils
creating build/lib.linux-x86_64-cpython-39/openfold/np
copying openfold/np/protein.py -> build/lib.linux-x86_64-cpython-39/openfold/np
copying openfold/np/residue_constants.py -> build/lib.linux-x86_64-cpython-39/openfold/np
copying openfold/np/init.py -> build/lib.linux-x86_64-cpython-39/openfold/np
creating build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/hhsearch.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/utils.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/kalign.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/hhblits.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/jackhmmer.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
copying openfold/data/tools/init.py -> build/lib.linux-x86_64-cpython-39/openfold/data/tools
creating build/lib.linux-x86_64-cpython-39/openfold/utils/kernel
copying openfold/utils/kernel/attention_core.py -> build/lib.linux-x86_64-cpython-39/openfold/utils/kernel
copying openfold/utils/kernel/init.py -> build/lib.linux-x86_64-cpython-39/openfold/utils/kernel
creating build/lib.linux-x86_64-cpython-39/openfold/np/relax
copying openfold/np/relax/amber_minimize.py -> build/lib.linux-x86_64-cpython-39/openfold/np/relax
copying openfold/np/relax/utils.py -> build/lib.linux-x86_64-cpython-39/openfold/np/relax
copying openfold/np/relax/cleanup.py -> build/lib.linux-x86_64-cpython-39/openfold/np/relax
copying openfold/np/relax/relax.py -> build/lib.linux-x86_64-cpython-39/openfold/np/relax
copying openfold/np/relax/init.py -> build/lib.linux-x86_64-cpython-39/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'
/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _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_kernel.cu -> 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.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.cpp -> 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
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/tmp/pip-install-jbp541x2/openfold_505a5225e2ba4112a59f2eb35c36361c/setup.py", line 74, in <module>
setup(
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/__init__.py", line 104, in setup
return distutils.core.setup(**attrs)
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 184, in setup
return run_commands(dist)
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 200, in run_commands
dist.run_commands()
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/dist.py", line 967, in run_command
super().run_command(command)
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 368, in run
self.run_command("build")
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/dist.py", line 967, in run_command
super().run_command(command)
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 132, in run
self.run_command(cmd_name)
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/dist.py", line 967, in run_command
super().run_command(command)
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/command/build_ext.py", line 91, in run
_build_ext.run(self)
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 359, in run
self.build_extensions()
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/torch/utils/cpp_extension.py", line 499, in build_extensions
_check_cuda_version(compiler_name, compiler_version)
File "/home/apps/anaconda3/envs/diffdock_test/lib/python3.9/site-packages/torch/utils/cpp_extension.py", line 386, in _check_cuda_version
raise RuntimeError(CUDA_MISMATCH_MESSAGE.format(cuda_str_version, torch.version.cuda))
RuntimeError:
The detected CUDA version (12.0) mismatches the version that was used to compile
PyTorch (11.7). 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
Failed to build openfold
ERROR: Could not build wheels for openfold, which is required to install pyproject.toml-based projects
from diffdock.
lzygitk7
commented on September 28, 2024
same here
...
...
...
RuntimeError:
The detected CUDA version (12.4) mismatches the version that was used to compile
PyTorch (11.7). Please make sure to use the same CUDA versions.
by running
pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git', while my cuda-runtime in related conda env is 11.7
Does anyone have any idea?
from diffdock.
Related Issues (20)
- The "skip" issue encountered after running the inference HOT 7
- spyrmsd dependency, why not installed with pip ? HOT 1
- Problem with openfold installation. HOT 2
- a problem with running Graphical UI HOT 2
- Training large models using train.py
- error while running the inference example HOT 3
- How to replicate results? HOT 2
- installation problem/ running interface python : No module named 'torch' (How to install torch and its dependencies properly?) HOT 1
- Running inference on multiple GPUS HOT 2
- _LinAlgErr when running inference HOT 2
- Failed on different complexes for inference.py on CPU and GPU are different for different batch size HOT 4
- Running without docker HOT 1
- errors when to run inference.py with vesion 1.1.2 HOT 1
- Side chains relevance in DiffDock predictions
- bfloat16 version of Diffdock
- Float division by zero on CUDA memory outage
- Web UI 'Samples Per Complex' Input Not Reflecting Changes
- ValueError: No edges and no nodes HOT 3
- Logger index error out of range
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from diffdock.