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Installation error on macOS
See original GitHub issueIssue
pip install torch-scatter fails on macOS, within a conda environment with Python 3.6.
Error
Collecting torch-scatter
Using cached https://files.pythonhosted.org/packages/30/d9/1d5fd4d183dabd9e0a1f7008ecf83318432359f4cc27480e3f2212f44d9c/torch_scatter-1.3.2.tar.gz
Building wheels for collected packages: torch-scatter
Building wheel for torch-scatter (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Users/rmeli/miniconda3/envs/py36t/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/r0/2dklzyn57d59g13_21b6kt7h0000gp/T/pip-install-24jrv0_u/torch-scatter/setup.py'"'"'; __file__='"'"'/private/var/folders/r0/2dklzyn57d59g13_21b6kt7h0000gp/T/pip-install-24jrv0_u/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 /private/var/folders/r0/2dklzyn57d59g13_21b6kt7h0000gp/T/pip-wheel-js5n7cck --python-tag cp36
cwd: /private/var/folders/r0/2dklzyn57d59g13_21b6kt7h0000gp/T/pip-install-24jrv0_u/torch-scatter/
Complete output (60 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.6
creating build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_std.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_max_min.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_broadcasting.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_multi_gpu.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_forward.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/utils.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_backward.py -> build/lib.macosx-10.7-x86_64-3.6/test
creating build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/max.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/add.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/div.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/std.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/min.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/mean.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/mul.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/sub.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
creating build/lib.macosx-10.7-x86_64-3.6/torch_scatter/utils
copying torch_scatter/utils/gen.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter/utils
copying torch_scatter/utils/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter/utils
copying torch_scatter/utils/ext.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter/utils
running build_ext
/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/utils/cpp_extension.py:172: UserWarning:
!! WARNING !!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Your compiler (g++) is not compatible with the compiler Pytorch was
built with for this platform, which is clang++ on darwin. Please
use clang++ to to compile your extension. Alternatively, you may
compile PyTorch from source using g++, and then you can also use
g++ to compile your extension.
See https://github.com/pytorch/pytorch/blob/master/CONTRIBUTING.md for help
with compiling PyTorch from source.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! WARNING !!
platform=sys.platform))
building 'torch_scatter.scatter_cpu' extension
creating build/temp.macosx-10.7-x86_64-3.6
creating build/temp.macosx-10.7-x86_64-3.6/cpu
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/rmeli/miniconda3/envs/py36t/include -arch x86_64 -I/Users/rmeli/miniconda3/envs/py36t/include -arch x86_64 -I/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include -I/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/torch/csrc/api/include -I/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/TH -I/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/THC -I/Users/rmeli/miniconda3/envs/py36t/include/python3.6m -c cpu/scatter.cpp -o build/temp.macosx-10.7-x86_64-3.6/cpu/scatter.o -Wno-unused-variable -DVERSION_GE_1_3 -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=scatter_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++11
warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
In file included from cpu/scatter.cpp:1:
In file included from /Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/torch/extension.h:4:
In file included from /Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/torch/csrc/api/include/torch/all.h:3:
/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/torch/csrc/api/include/torch/cuda.h:5:10: fatal error: 'cstddef' file not found
#include <cstddef>
^~~~~~~~~
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for torch-scatter
Running setup.py clean for torch-scatter
Failed to build torch-scatter
Installing collected packages: torch-scatter
Running setup.py install for torch-scatter ... error
ERROR: Command errored out with exit status 1:
command: /Users/rmeli/miniconda3/envs/py36t/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/r0/2dklzyn57d59g13_21b6kt7h0000gp/T/pip-install-24jrv0_u/torch-scatter/setup.py'"'"'; __file__='"'"'/private/var/folders/r0/2dklzyn57d59g13_21b6kt7h0000gp/T/pip-install-24jrv0_u/torch-scatter/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/r0/2dklzyn57d59g13_21b6kt7h0000gp/T/pip-record-h3mh8ud7/install-record.txt --single-version-externally-managed --compile
cwd: /private/var/folders/r0/2dklzyn57d59g13_21b6kt7h0000gp/T/pip-install-24jrv0_u/torch-scatter/
Complete output (60 lines):
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.6
creating build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_std.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_max_min.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_broadcasting.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_multi_gpu.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_forward.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/utils.py -> build/lib.macosx-10.7-x86_64-3.6/test
copying test/test_backward.py -> build/lib.macosx-10.7-x86_64-3.6/test
creating build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/max.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/add.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/div.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/std.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/min.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/mean.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/mul.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
copying torch_scatter/sub.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter
creating build/lib.macosx-10.7-x86_64-3.6/torch_scatter/utils
copying torch_scatter/utils/gen.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter/utils
copying torch_scatter/utils/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter/utils
copying torch_scatter/utils/ext.py -> build/lib.macosx-10.7-x86_64-3.6/torch_scatter/utils
running build_ext
/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/utils/cpp_extension.py:172: UserWarning:
!! WARNING !!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Your compiler (g++) is not compatible with the compiler Pytorch was
built with for this platform, which is clang++ on darwin. Please
use clang++ to to compile your extension. Alternatively, you may
compile PyTorch from source using g++, and then you can also use
g++ to compile your extension.
See https://github.com/pytorch/pytorch/blob/master/CONTRIBUTING.md for help
with compiling PyTorch from source.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! WARNING !!
platform=sys.platform))
building 'torch_scatter.scatter_cpu' extension
creating build/temp.macosx-10.7-x86_64-3.6
creating build/temp.macosx-10.7-x86_64-3.6/cpu
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/rmeli/miniconda3/envs/py36t/include -arch x86_64 -I/Users/rmeli/miniconda3/envs/py36t/include -arch x86_64 -I/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include -I/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/torch/csrc/api/include -I/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/TH -I/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/THC -I/Users/rmeli/miniconda3/envs/py36t/include/python3.6m -c cpu/scatter.cpp -o build/temp.macosx-10.7-x86_64-3.6/cpu/scatter.o -Wno-unused-variable -DVERSION_GE_1_3 -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=scatter_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++11
warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
In file included from cpu/scatter.cpp:1:
In file included from /Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/torch/extension.h:4:
In file included from /Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/torch/csrc/api/include/torch/all.h:3:
/Users/rmeli/miniconda3/envs/py36t/lib/python3.6/site-packages/torch/include/torch/csrc/api/include/torch/cuda.h:5:10: fatal error: 'cstddef' file not found
#include <cstddef>
^~~~~~~~~
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/rmeli/miniconda3/envs/py36t/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/r0/2dklzyn57d59g13_21b6kt7h0000gp/T/pip-install-24jrv0_u/torch-scatter/setup.py'"'"'; __file__='"'"'/private/var/folders/r0/2dklzyn57d59g13_21b6kt7h0000gp/T/pip-install-24jrv0_u/torch-scatter/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/r0/2dklzyn57d59g13_21b6kt7h0000gp/T/pip-record-h3mh8ud7/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
Environment
conda create -n py36 python=3.6 pip
conda activate py36
conda install pytorch=1.3 -c pytorch
Additional Details
Python 3.7
Using Python 3.7 istead of 3.6 does not fail…
conda create -n py37 python=3.7 pip
conda activate py37
conda install pytorch=1.3 -c pytorch
pip install torch-scatter
Processing /Users/rmeli/Library/Caches/pip/wheels/40/30/07/5400c1a1ec05c5d0d6459fb2179d0e12c7c2f6d3d47987bf10/torch_scatter-1.3.2-cp37-cp37m-macosx_10_9_x86_64.whl
Installing collected packages: torch-scatter
Successfully installed torch-scatter-1.3.2
Linux
I have CI setup on a private repo where I’m trying to use pytorch_goemteric. This error occours only with macOS builds using Python 3.6 (both with xcode11 and xcode10). Linux builds work normally (both versions of Python, both Xenial and Bionic).
Issue Analytics
- State:
- Created 4 years ago
- Comments:5 (3 by maintainers)
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Ah I see, that’s interesting. I added this note to the documentation.
I think this is the reason, which is very strange. Using Python
3.7works (both on Travis CI and locally), but the reported error happens with3.6.