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Failed to build wheel for torch-scatter: ERROR: Command errored out with exit status 1:

See original GitHub issue

📚 Installation

Environment

  • OS: Ubuntu 18.04
  • Python version: 3.7.7
  • PyTorch version: 1.5.1
  • CUDA/cuDNN version: 10.1
  • GCC version: 7.5.0
  • How did you try to install PyTorch Geometric and its extensions (wheel, source): source
  • Any other relevant information: Graphic Card-GTX 1060, Driver version-440

Checklist

  • [ ~ ] I followed the installation guide.
  • [ ~ ] I cannot find my error message in the FAQ.
  • [ ~ ] I set up CUDA correctly and can compile CUDA code via nvcc.
  • [ ~ ] I do have multiple CUDA versions on my machine.

Additional context

Hi! I’m trying to install PyTorch Geometric on my Ubuntu 18.04 server. However, when I install it through the official guidance, this error happens. I cannot find it in the frequency Q&A. Could you please help me with this? Thank you so much in advance.

Further Details:

To avoid possible problems, I do these preparation works before I installed:

  • My CUDA version, cuDNN version and PyTorch version are all matched. (10.1)
  • No multiple CUDA in my system. Only CUDA 10.1 is installed. (As well as matched cuDNN)
  • I add all the path, just follow the instructions.
  • nvcc is accessible from the terminal.

However, when I start with pip install torch-scatter, error happens.

Here are the details of my errors:

~/anaconda3/envs/pytorch101$ pip install torch-scatter
Collecting torch-scatter
  Downloading torch_scatter-2.0.5.tar.gz (20 kB)
Building wheels for collected packages: torch-scatter

  Building wheel for torch-scatter (setup.py) ... error

  ERROR: Command errored out with exit status 1:

   command: /home/zihan/anaconda3/envs/pytorch101/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-jeo_88fj/torch-scatter/setup.py'"'"'; __file__='"'"'/tmp/pip-install-jeo_88fj/torch-scatter/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-wmjvsyru
       cwd: /tmp/pip-install-jeo_88fj/torch-scatter/
  Complete output (108 lines):
  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/torch_scatter
  copying torch_scatter/segment_coo.py -> build/lib.linux-x86_64-3.7/torch_scatter
  copying torch_scatter/utils.py -> build/lib.linux-x86_64-3.7/torch_scatter
  copying torch_scatter/placeholder.py -> build/lib.linux-x86_64-3.7/torch_scatter
  copying torch_scatter/segment_csr.py -> build/lib.linux-x86_64-3.7/torch_scatter
  copying torch_scatter/__init__.py -> build/lib.linux-x86_64-3.7/torch_scatter
  copying torch_scatter/scatter.py -> build/lib.linux-x86_64-3.7/torch_scatter
  creating build/lib.linux-x86_64-3.7/torch_scatter/composite
  copying torch_scatter/composite/logsumexp.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
  copying torch_scatter/composite/__init__.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
  copying torch_scatter/composite/softmax.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
  copying torch_scatter/composite/std.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
  running build_ext
  building 'torch_scatter._scatter' extension
  creating build/temp.linux-x86_64-3.7
  creating build/temp.linux-x86_64-3.7/tmp
  creating build/temp.linux-x86_64-3.7/tmp/pip-install-jeo_88fj
  creating build/temp.linux-x86_64-3.7/tmp/pip-install-jeo_88fj/torch-scatter
  creating build/temp.linux-x86_64-3.7/tmp/pip-install-jeo_88fj/torch-scatter/csrc
  creating build/temp.linux-x86_64-3.7/tmp/pip-install-jeo_88fj/torch-scatter/csrc/cpu
  creating build/temp.linux-x86_64-3.7/tmp/pip-install-jeo_88fj/torch-scatter/csrc/cuda
  gcc -pthread -B /home/zihan/anaconda3/envs/pytorch101/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_CUDA -I/tmp/pip-install-jeo_88fj/torch-scatter/csrc -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/TH -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/THC -I/usr/local/cuda/include -I/home/zihan/anaconda3/envs/pytorch101/include/python3.7m -c /tmp/pip-install-jeo_88fj/torch-scatter/csrc/scatter.cpp -o build/temp.linux-x86_64-3.7/tmp/pip-install-jeo_88fj/torch-scatter/csrc/scatter.o -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_scatter -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++
  gcc -pthread -B /home/zihan/anaconda3/envs/pytorch101/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_CUDA -I/tmp/pip-install-jeo_88fj/torch-scatter/csrc -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/TH -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/THC -I/usr/local/cuda/include -I/home/zihan/anaconda3/envs/pytorch101/include/python3.7m -c /tmp/pip-install-jeo_88fj/torch-scatter/csrc/cpu/scatter_cpu.cpp -o build/temp.linux-x86_64-3.7/tmp/pip-install-jeo_88fj/torch-scatter/csrc/cpu/scatter_cpu.o -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_scatter -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++
  /usr/local/cuda/bin/nvcc -DWITH_CUDA -I/tmp/pip-install-jeo_88fj/torch-scatter/csrc -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/TH -I/home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/THC -I/usr/local/cuda/include -I/home/zihan/anaconda3/envs/pytorch101/include/python3.7m -c /tmp/pip-install-jeo_88fj/torch-scatter/csrc/cuda/scatter_cuda.cu -o build/temp.linux-x86_64-3.7/tmp/pip-install-jeo_88fj/torch-scatter/csrc/cuda/scatter_cuda.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options '-fPIC' -arch=sm_35 --expt-relaxed-constexpr -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_scatter -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(14): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(15): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(15): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(15): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(18): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(19): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(19): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(19): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(23): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(24): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(24): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(24): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/autograd/profiler.h(100): warning: attribute "__visibility__" does not apply here
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/autograd/profiler.h(115): warning: attribute "__visibility__" does not apply here
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/enum.h(187): warning: statement is unreachable
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/enum.h(187): warning: statement is unreachable
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(14): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(15): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(15): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(15): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(18): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(19): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(19): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(19): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(23): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(24): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(24): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/functional/padding.h(24): warning: integer conversion resulted in a change of sign
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/autograd/profiler.h(100): warning: attribute "__visibility__" does not apply here
  
  /home/zihan/anaconda3/envs/pytorch101/lib/python3.7/site-packages/torch/include/torch/csrc/autograd/profiler.h(115): warning: attribute "__visibility__" does not apply here
  
  /usr/include/c++/7/bits/basic_string.tcc: In instantiation of ‘static std::basic_string<_CharT, _Traits, _Alloc>::_Rep* std::basic_string<_CharT, _Traits, _Alloc>::_Rep::_S_create(std::basic_string<_CharT, _Traits, _Alloc>::size_type, std::basic_string<_CharT, _Traits, _Alloc>::size_type, const _Alloc&) [with _CharT = char16_t; _Traits = std::char_traits<char16_t>; _Alloc = std::allocator<char16_t>; std::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]’:
  /usr/include/c++/7/bits/basic_string.tcc:578:28:   required from ‘static _CharT* std::basic_string<_CharT, _Traits, _Alloc>::_S_construct(_InIterator, _InIterator, const _Alloc&, std::forward_iterator_tag) [with _FwdIterator = const char16_t*; _CharT = char16_t; _Traits = std::char_traits<char16_t>; _Alloc = std::allocator<char16_t>]’
  /usr/include/c++/7/bits/basic_string.h:5042:20:   required from ‘static _CharT* std::basic_string<_CharT, _Traits, _Alloc>::_S_construct_aux(_InIterator, _InIterator, const _Alloc&, std::__false_type) [with _InIterator = const char16_t*; _CharT = char16_t; _Traits = std::char_traits<char16_t>; _Alloc = std::allocator<char16_t>]’
  /usr/include/c++/7/bits/basic_string.h:5063:24:   required from ‘static _CharT* std::basic_string<_CharT, _Traits, _Alloc>::_S_construct(_InIterator, _InIterator, const _Alloc&) [with _InIterator = const char16_t*; _CharT = char16_t; _Traits = std::char_traits<char16_t>; _Alloc = std::allocator<char16_t>]’
  /usr/include/c++/7/bits/basic_string.tcc:656:134:   required from ‘std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, std::basic_string<_CharT, _Traits, _Alloc>::size_type, const _Alloc&) [with _CharT = char16_t; _Traits = std::char_traits<char16_t>; _Alloc = std::allocator<char16_t>; std::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]’
  /usr/include/c++/7/bits/basic_string.h:6688:95:   required from here
  /usr/include/c++/7/bits/basic_string.tcc:1067:16: error: cannot call member function ‘void std::basic_string<_CharT, _Traits, _Alloc>::_Rep::_M_set_sharable() [with _CharT = char16_t; _Traits = std::char_traits<char16_t>; _Alloc = std::allocator<char16_t>]’ without object
         __p->_M_set_sharable();
         ~~~~~~~~~^~
  /usr/include/c++/7/bits/basic_string.tcc: In instantiation of ‘static std::basic_string<_CharT, _Traits, _Alloc>::_Rep* std::basic_string<_CharT, _Traits, _Alloc>::_Rep::_S_create(std::basic_string<_CharT, _Traits, _Alloc>::size_type, std::basic_string<_CharT, _Traits, _Alloc>::size_type, const _Alloc&) [with _CharT = char32_t; _Traits = std::char_traits<char32_t>; _Alloc = std::allocator<char32_t>; std::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]’:
  /usr/include/c++/7/bits/basic_string.tcc:578:28:   required from ‘static _CharT* std::basic_string<_CharT, _Traits, _Alloc>::_S_construct(_InIterator, _InIterator, const _Alloc&, std::forward_iterator_tag) [with _FwdIterator = const char32_t*; _CharT = char32_t; _Traits = std::char_traits<char32_t>; _Alloc = std::allocator<char32_t>]’
  /usr/include/c++/7/bits/basic_string.h:5042:20:   required from ‘static _CharT* std::basic_string<_CharT, _Traits, _Alloc>::_S_construct_aux(_InIterator, _InIterator, const _Alloc&, std::__false_type) [with _InIterator = const char32_t*; _CharT = char32_t; _Traits = std::char_traits<char32_t>; _Alloc = std::allocator<char32_t>]’
  /usr/include/c++/7/bits/basic_string.h:5063:24:   required from ‘static _CharT* std::basic_string<_CharT, _Traits, _Alloc>::_S_construct(_InIterator, _InIterator, const _Alloc&) [with _InIterator = const char32_t*; _CharT = char32_t; _Traits = std::char_traits<char32_t>; _Alloc = std::allocator<char32_t>]’
  /usr/include/c++/7/bits/basic_string.tcc:656:134:   required from ‘std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, std::basic_string<_CharT, _Traits, _Alloc>::size_type, const _Alloc&) [with _CharT = char32_t; _Traits = std::char_traits<char32_t>; _Alloc = std::allocator<char32_t>; std::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]’
  /usr/include/c++/7/bits/basic_string.h:6693:95:   required from here
  /usr/include/c++/7/bits/basic_string.tcc:1067:16: error: cannot call member function ‘void std::basic_string<_CharT, _Traits, _Alloc>::_Rep::_M_set_sharable() [with _CharT = char32_t; _Traits = std::char_traits<char32_t>; _Alloc = std::allocator<char32_t>]’ without object
  error: command '/usr/local/cuda/bin/nvcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for torch-scatter

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Comments:9 (3 by maintainers)

github_iconTop GitHub Comments

1reaction
rusty1scommented, Jun 7, 2021

Since PyG is quite “old” already, we supported all PyTorch versions >= 0.4 at some point in time (with torch-geometric, torch-scatter, … having specific version requirements). I will curate a list of version dependencies at some point in time 😃

1reaction
ZihanChen1995commented, Jun 5, 2021

Mind sharing how you solved the problem? @ZihanChen1995 Thank you.

Hi, at that time, I just downgraded the PyTorch version and it works.

Read more comments on GitHub >

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