/usr/include/c++/6/cmath:45:23: fatal error: math.h: No such file or directory #106

sbelharbi · 2019-03-21T16:07:03Z

Hi,
config:
Ubuntu: 18.04
gcc: 5.5, 6.5, 7.3
cuda: 9.1
python: 3.7
pytorch: 1.0

This issue is related to some posted issues. Sorry for repetition.

I am sure the error is related to the version of cuda, gcc. For now, I changed the version of gcc (using update-alternatives) and the wheel of pytorch (compiled using different cuda).

I obtain the error below. Any pointer is much appreciated!!! thanks
Since the error points to missing headers, I reinstalled:

sudo apt install --reinstall libstdc++-{5, 6, 7}-dev.

But the error persists.

Traceback (most recent call last):
  File "/home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 946, in _build_extension_module
    check=True)
  File "/home/brian/anaconda3/lib/python3.7/subprocess.py", line 468, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3291, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-2-99c8874721c0>", line 1, in <module>
    runfile('/mnt/0890ce70-3387-4496-a36e-fe2ed1d8596f/research/code/glas-1/test.py', wdir='/mnt/0890ce70-3387-4496-a36e-fe2ed1d8596f/research/code/glas-1')
  File "/home/brian/.local/share/JetBrains/Toolbox/apps/PyCharm-P/ch-0/183.5912.18/helpers/pydev/_pydev_bundle/pydev_umd.py", line 197, in runfile
    pydev_imports.execfile(filename, global_vars, local_vars)  # execute the script
  File "/home/brian/.local/share/JetBrains/Toolbox/apps/PyCharm-P/ch-0/183.5912.18/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "/mnt/0890ce70-3387-4496-a36e-fe2ed1d8596f/research/code/glas-1/test.py", line 3, in <module>
    from deepmil.deeplabv3 import Res_Deeplab
  File "/home/brian/.local/share/JetBrains/Toolbox/apps/PyCharm-P/ch-0/183.5912.18/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "/mnt/0890ce70-3387-4496-a36e-fe2ed1d8596f/research/code/glas-1/deepmil/deeplabv3.py", line 17, in <module>
    from libs import InPlaceABN, InPlaceABNSync
  File "/home/brian/.local/share/JetBrains/Toolbox/apps/PyCharm-P/ch-0/183.5912.18/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "/mnt/0890ce70-3387-4496-a36e-fe2ed1d8596f/research/code/glas-1/libs/__init__.py", line 1, in <module>
    from .bn import ABN, InPlaceABN, InPlaceABNSync
  File "/home/brian/.local/share/JetBrains/Toolbox/apps/PyCharm-P/ch-0/183.5912.18/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "/mnt/0890ce70-3387-4496-a36e-fe2ed1d8596f/research/code/glas-1/libs/bn.py", line 10, in <module>
    from .functions import *
  File "/home/brian/.local/share/JetBrains/Toolbox/apps/PyCharm-P/ch-0/183.5912.18/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "/mnt/0890ce70-3387-4496-a36e-fe2ed1d8596f/research/code/glas-1/libs/functions.py", line 18, in <module>
    extra_cuda_cflags=["--expt-extended-lambda"])
  File "/home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 645, in load
    is_python_module)
  File "/home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 814, in _jit_compile
    with_cuda=with_cuda)
  File "/home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 863, in _write_ninja_file_and_build
    _build_extension_module(name, build_directory, verbose)
  File "/home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 959, in _build_extension_module
    raise RuntimeError(message)
RuntimeError: Error building extension 'inplace_abn': [1/3] /usr/bin/nvcc -DTORCH_EXTENSION_NAME=inplace_abn -DTORCH_API_INCLUDE_EXTENSION_H -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/torch/csrc/api/include -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/TH -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/THC -isystem /usr/include -isystem /home/brian/Venvs/pytorch.1.0.1/include/python3.7m -D_GLIBCXX_USE_CXX11_ABI=0 -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --compiler-options '-fPIC' --expt-extended-lambda -std=c++11 -c /mnt/0890ce70-3387-4496-a36e-fe2ed1d8596f/research/code/glas-1/libs/src/inplace_abn_cuda.cu -o inplace_abn_cuda.cuda.o
FAILED: inplace_abn_cuda.cuda.o 
/usr/bin/nvcc -DTORCH_EXTENSION_NAME=inplace_abn -DTORCH_API_INCLUDE_EXTENSION_H -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/torch/csrc/api/include -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/TH -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/THC -isystem /usr/include -isystem /home/brian/Venvs/pytorch.1.0.1/include/python3.7m -D_GLIBCXX_USE_CXX11_ABI=0 -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --compiler-options '-fPIC' --expt-extended-lambda -std=c++11 -c /mnt/0890ce70-3387-4496-a36e-fe2ed1d8596f/research/code/glas-1/libs/src/inplace_abn_cuda.cu -o inplace_abn_cuda.cuda.o
In file included from /usr/include/crt/math_functions.h:8835:0,
                 from /usr/include/crt/common_functions.h:271,
                 from /usr/include/common_functions.h:50,
                 from /usr/include/cuda_runtime.h:115,
                 from <command-line>:0:
/usr/include/c++/6/cmath:45:23: fatal error: math.h: No such file or directory
 #include_next <math.h>
                       ^
compilation terminated.
[2/3] /usr/bin/nvcc -DTORCH_EXTENSION_NAME=inplace_abn -DTORCH_API_INCLUDE_EXTENSION_H -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/torch/csrc/api/include -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/TH -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/THC -isystem /usr/include -isystem /home/brian/Venvs/pytorch.1.0.1/include/python3.7m -D_GLIBCXX_USE_CXX11_ABI=0 -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --compiler-options '-fPIC' --expt-extended-lambda -std=c++11 -c /mnt/0890ce70-3387-4496-a36e-fe2ed1d8596f/research/code/glas-1/libs/src/inplace_abn_cuda_half.cu -o inplace_abn_cuda_half.cuda.o
FAILED: inplace_abn_cuda_half.cuda.o 
/usr/bin/nvcc -DTORCH_EXTENSION_NAME=inplace_abn -DTORCH_API_INCLUDE_EXTENSION_H -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/torch/csrc/api/include -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/TH -isystem /home/brian/Venvs/pytorch.1.0.1/lib/python3.7/site-packages/torch/lib/include/THC -isystem /usr/include -isystem /home/brian/Venvs/pytorch.1.0.1/include/python3.7m -D_GLIBCXX_USE_CXX11_ABI=0 -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --compiler-options '-fPIC' --expt-extended-lambda -std=c++11 -c /mnt/0890ce70-3387-4496-a36e-fe2ed1d8596f/research/code/glas-1/libs/src/inplace_abn_cuda_half.cu -o inplace_abn_cuda_half.cuda.o
In file included from /usr/include/crt/math_functions.h:8835:0,
                 from /usr/include/crt/common_functions.h:271,
                 from /usr/include/common_functions.h:50,
                 from /usr/include/cuda_runtime.h:115,
                 from <command-line>:0:
/usr/include/c++/6/cmath:45:23: fatal error: math.h: No such file or directory
 #include_next <math.h>
                       ^
compilation terminated.
ninja: build stopped: subcommand failed.

sbelharbi · 2019-03-22T01:18:52Z

Fixed.
Cause of the issue: mismatch of the gcc, cuda versions (pytorch pre-compiled version made things worse).

Ubuntu: 18.04

Fix:

Install cuda 10.0 (https://developer.nvidia.com/cuda-10.0-download-archive)
Switch to gcc 7.3 (if you have many versions of gcc use update-alternatives. Ubuntu 18.04 comes by default with gcc 7.3.)
Install the pytoch wheel for the version 1.0.0 for cuda 10.0: cu100/torch-1.0.0-cp37-cp37m-linux_x86_64.whl
If you have many versions of cuda: add the following to ~/.bashrc and specify the cuda version you intend to use:

CUDAVER=cuda-10.0
export PATH=/usr/local/$CUDAVER/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/$CUDAVER/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/usr/local/$CUDAVER/lib64:$LD_LIBRARY_PATH
export CUDA_PATH=/usr/local/$CUDAVER
export CUDA_ROOT=/usr/local/$CUDAVER
export CUDA_HOME=/usr/local/$CUDAVER
export CUDA_HOST_COMPILER=/usr/bin/gcc-7.3

Closed.

coderbusy7 · 2021-02-05T15:32:49Z

To include files, use isystem instead of I. That's it!

8secz-johndpope · 2021-02-05T19:29:01Z

cudatoolkit 11.2 / or change to latest version - https://developer.nvidia.com/Cuda-downloads

add to ~/.bashrc or ~/.zshrc

CUDAVER=cuda-11.2
export PATH=/usr/local/$CUDAVER/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/$CUDAVER/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/usr/local/$CUDAVER/lib64:$LD_LIBRARY_PATH
export CUDA_PATH=/usr/local/$CUDAVER
export CUDA_ROOT=/usr/local/$CUDAVER
export CUDA_HOME=/usr/local/$CUDAVER
export CUDA_HOST_COMPILER=/usr/bin/gcc-10

sbelharbi closed this as completed Mar 22, 2019

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/usr/include/c++/6/cmath:45:23: fatal error: math.h: No such file or directory #106

/usr/include/c++/6/cmath:45:23: fatal error: math.h: No such file or directory #106

sbelharbi commented Mar 21, 2019 •

edited

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sbelharbi commented Mar 22, 2019

coderbusy7 commented Feb 5, 2021

8secz-johndpope commented Feb 5, 2021

/usr/include/c++/6/cmath:45:23: fatal error: math.h: No such file or directory #106

/usr/include/c++/6/cmath:45:23: fatal error: math.h: No such file or directory #106

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sbelharbi commented Mar 21, 2019 • edited Loading

sbelharbi commented Mar 22, 2019

coderbusy7 commented Feb 5, 2021

8secz-johndpope commented Feb 5, 2021

sbelharbi commented Mar 21, 2019 •

edited

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