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Error building docker image

See original GitHub issue

From now on, we recommend using our discussion forum (https://github.com/rusty1s/pytorch_geometric/discussions) for general questions.

❓ Questions & Help

I am using the Dockerfile within this repo. However, when I try to build the image myself. I encountered the ‘gcc error’. pyG temporal docker error

The full error log would be:

  ERROR: Command errored out with exit status 1:
   command: /home/user/miniconda/envs/py36/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/setup.py'"'"'; __file__='"'"'/tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-0dqbqa0s
       cwd: /tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/
  Complete output (58 lines):
  No CUDA runtime is found, using CUDA_HOME='/usr/local/cuda'
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.6
  creating build/lib.linux-x86_64-3.6/torch_scatter
  copying torch_scatter/segment_csr.py -> build/lib.linux-x86_64-3.6/torch_scatter
  copying torch_scatter/scatter.py -> build/lib.linux-x86_64-3.6/torch_scatter
  copying torch_scatter/segment_coo.py -> build/lib.linux-x86_64-3.6/torch_scatter
  copying torch_scatter/utils.py -> build/lib.linux-x86_64-3.6/torch_scatter
  copying torch_scatter/__init__.py -> build/lib.linux-x86_64-3.6/torch_scatter
  copying torch_scatter/placeholder.py -> build/lib.linux-x86_64-3.6/torch_scatter
  creating build/lib.linux-x86_64-3.6/torch_scatter/composite
  copying torch_scatter/composite/logsumexp.py -> build/lib.linux-x86_64-3.6/torch_scatter/composite
  copying torch_scatter/composite/std.py -> build/lib.linux-x86_64-3.6/torch_scatter/composite
  copying torch_scatter/composite/__init__.py -> build/lib.linux-x86_64-3.6/torch_scatter/composite
  copying torch_scatter/composite/softmax.py -> build/lib.linux-x86_64-3.6/torch_scatter/composite
  running build_ext
  building 'torch_scatter._version_cpu' extension
  creating build/temp.linux-x86_64-3.6
  creating build/temp.linux-x86_64-3.6/tmp
  creating build/temp.linux-x86_64-3.6/tmp/pip-install-fssw7td4
  creating build/temp.linux-x86_64-3.6/tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85
  creating build/temp.linux-x86_64-3.6/tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc
  gcc -pthread -B /home/user/miniconda/envs/py36/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc -I/home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include -I/home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/torch/csrc/api/include -I/home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/TH -I/home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/THC -I/home/user/miniconda/envs/py36/include/python3.6m -c /tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc/version.cpp -o build/temp.linux-x86_64-3.6/tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc/version.o -O2 -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_version_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++11
  cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
  In file included from /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/boxing/KernelFunction.h:5:0,
                   from /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/dispatch/DispatchTable.h:10,
                   from /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/dispatch/OperatorEntry.h:3,
                   from /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/dispatch/Dispatcher.h:3,
                   from /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/TensorMethods.h:10,
                   from /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/Tensor.h:12,
                   from /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/Context.h:4,
                   from /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/ATen.h:5,
                   from /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/torch/csrc/api/include/torch/types.h:3,
                   from /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/torch/script.h:3,
                   from /tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc/version.cpp:2:
  /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/boxing/kernel_functor.h: In instantiation of 'typename c10::guts::infer_function_traits<Functor>::type::return_type c10::detail::call_functor_with_args_from_stack_(Functor*, c10::Stack*, c10::guts::index_sequence<INDEX ...>) [with Functor = c10::detail::WrapRuntimeKernelFunctor_<long int (*)(), long int, c10::guts::typelist::typelist<> >; bool AllowDeprecatedTypes = true; long unsigned int ...ivalue_arg_indices = {}; typename c10::guts::infer_function_traits<Functor>::type::return_type = long int; c10::Stack = std::vector<c10::IValue, std::allocator<c10::IValue> >; c10::guts::index_sequence<INDEX ...> = c10::guts::integer_sequence<long unsigned int>]':
  /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/boxing/kernel_functor.h:202:77:   required from 'typename c10::guts::infer_function_traits<Functor>::type::return_type c10::detail::call_functor_with_args_from_stack(Functor*, c10::Stack*) [with Functor = c10::detail::WrapRuntimeKernelFunctor_<long int (*)(), long int, c10::guts::typelist::typelist<> >; bool AllowDeprecatedTypes = true; typename c10::guts::infer_function_traits<Functor>::type::return_type = long int; c10::Stack = std::vector<c10::IValue, std::allocator<c10::IValue> >]'
  /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/boxing/kernel_functor.h:234:91:   required from 'static void c10::detail::wrap_kernel_functor_boxed<KernelFunctor, AllowDeprecatedTypes, typename std::enable_if<(! std::is_same<void, typename c10::guts::infer_function_traits<Functor>::type::return_type>::value), void>::type>::call(c10::OperatorKernel*, c10::Stack*) [with KernelFunctor = c10::detail::WrapRuntimeKernelFunctor_<long int (*)(), long int, c10::guts::typelist::typelist<> >; bool AllowDeprecatedTypes = true; c10::Stack = std::vector<c10::IValue, std::allocator<c10::IValue> >]'
  /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/boxing/KernelFunction.h:172:7:   required from 'static c10::KernelFunction c10::KernelFunction::makeFromUnboxedFunctor(std::unique_ptr<c10::OperatorKernel>) [with bool AllowLegacyTypes = true; KernelFunctor = c10::detail::WrapRuntimeKernelFunctor_<long int (*)(), long int, c10::guts::typelist::typelist<> >]'
  /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/boxing/KernelFunction.h:313:111:   required from 'static c10::KernelFunction c10::KernelFunction::makeFromUnboxedRuntimeFunction(FuncType*) [with bool AllowLegacyTypes = true; FuncType = long int()]'
  /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/op_registration/op_registration.h:517:72:   required from 'c10::guts::enable_if_t<(c10::guts::is_function_type<T>::value && (! std::is_same<FuncType, void(c10::OperatorKernel*, std::vector<c10::IValue, std::allocator<c10::IValue> >*)>::value)), c10::RegisterOperators&&> c10::RegisterOperators::op(const string&, FuncType*, c10::RegisterOperators::Options&&) && [with FuncType = long int(); c10::guts::enable_if_t<(c10::guts::is_function_type<T>::value && (! std::is_same<FuncType, void(c10::OperatorKernel*, std::vector<c10::IValue, std::allocator<c10::IValue> >*)>::value)), c10::RegisterOperators&&> = c10::RegisterOperators&&; std::string = std::basic_string<char>]'
  /tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc/version.cpp:25:79:   required from here
  /home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/ATen/core/boxing/kernel_functor.h:191:22: warning: variable 'num_ivalue_args' set but not used [-Wunused-but-set-variable]
       constexpr size_t num_ivalue_args = sizeof...(ivalue_arg_indices);
                        ^~~~~~~~~~~~~~~
  g++ -pthread -shared -B /home/user/miniconda/envs/py36/compiler_compat -L/home/user/miniconda/envs/py36/lib -Wl,-rpath=/home/user/miniconda/envs/py36/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc/version.o -o build/lib.linux-x86_64-3.6/torch_scatter/_version_cpu.so -s
  building 'torch_scatter._segment_coo_cpu' extension
  creating build/temp.linux-x86_64-3.6/tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc/cpu
  gcc -pthread -B /home/user/miniconda/envs/py36/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc -I/home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include -I/home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/torch/csrc/api/include -I/home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/TH -I/home/user/miniconda/envs/py36/lib/python3.6/site-packages/torch/include/THC -I/home/user/miniconda/envs/py36/include/python3.6m -c /tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc/segment_coo.cpp -o build/temp.linux-x86_64-3.6/tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc/segment_coo.o -O2 -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_segment_coo_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++11
  cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
  /tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc/segment_coo.cpp: In static member function 'static torch::autograd::variable_list SegmentMeanCOO::backward(torch::autograd::AutogradContext*, torch::autograd::variable_list)':
  /tmp/pip-install-fssw7td4/torch-scatter_0d58cd9527cc4f64bcb7fe55c6dd4e85/csrc/segment_coo.cpp:104:13: error: 'class at::Tensor' has no member named 'true_divide_'
       grad_in.true_divide_(count);
               ^~~~~~~~~~~~
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for torch-scatter

Issue Analytics

State:
Created 2 years ago
Comments:5 (1 by maintainers)

Top GitHub Comments

1reaction

johnny12150commented, May 15, 2021

FROM nvidia/cuda:11.1.1-base-ubuntu20.04

# Install some basic utilities
RUN apt-get update && apt-get install -y \
    curl \
    ca-certificates \
    sudo \
    git \
    bzip2 \
    libx11-6 \
 && rm -rf /var/lib/apt/lists/*

# Create a working directory
RUN mkdir /app
WORKDIR /app

# Create a non-root user and switch to it
RUN adduser --disabled-password --gecos '' --shell /bin/bash user \
 && chown -R user:user /app
RUN echo "user ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/90-user
USER user

# All users can use /home/user as their home directory
ENV HOME=/home/user
RUN chmod 777 /home/user

# Install Miniconda and Python 3.8
ENV CONDA_AUTO_UPDATE_CONDA=false
ENV PATH=/home/user/miniconda/bin:$PATH
RUN curl -sLo ~/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-py38_4.8.3-Linux-x86_64.sh \
 && chmod +x ~/miniconda.sh \
 && ~/miniconda.sh -b -p ~/miniconda \
 && rm ~/miniconda.sh \
 && conda install -y python==3.8.3 \
 && conda clean -ya

# CUDA 11.1-specific steps
RUN conda install -y -c conda-forge cudatoolkit=11.1.1 \
 && conda install -y -c pytorch \
    "pytorch=1.8.1=py3.8_cuda11.1_cudnn8.0.5_0" \
    "torchvision=0.9.1=py38_cu111" \
 && conda clean -ya

# Install PyTorch Geometric.
RUN CPATH=/usr/local/cuda/include:$CPATH \
 && LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH \
 && DYLD_LIBRARY_PATH=/usr/local/cuda/lib:$DYLD_LIBRARY_PATH

RUN pip install scipy

RUN pip install --no-index torch-scatter -f https://pytorch-geometric.com/whl/torch-1.8.0+cu111.html \
 && pip install --no-index torch-sparse -f https://pytorch-geometric.com/whl/torch-1.8.0+cu111.html \
 && pip install --no-index torch-cluster -f https://pytorch-geometric.com/whl/torch-1.8.0+cu111.html \
 && pip install --no-index torch-spline-conv -f https://pytorch-geometric.com/whl/torch-1.8.0+cu111.html \
 && pip install torch-geometric

# Set the default command to python3
CMD ["python3"]

This works for me. Hope it will help someone who needs an image of this.

0reactions

Haggaimcommented, Sep 5, 2021

Worked for me as well. Thanks fo sharing!