fatal error: pybind11/pybind11.h: No such file or directory #2

chadgh · 2016-05-19T14:52:40Z

I tried following the example in the README and got the following error:

/tmp/tmp826vncgj/somecode.cpp:2:36: fatal error: pybind11/pybind11.h: No such file or directory
     #include <pybind11/pybind11.h>

The text was updated successfully, but these errors were encountered:

tbenthompson · 2016-05-19T15:13:55Z

This is a problem with the installation. The pybind11 dependency isn't being found. It's hard to easily say what the problem is.

Some quick questions:

Did you use pip to install?
Operating system?
Python version?
Virtualenv? Conda environment? Anything like that?

Would you be willing to run these lines and then list the files in the folders that are output for me?

>>> import pybind11
>>> pybind11.get_include()
'/usr/local/include/python2.7'
>>> pybind11.get_include(True)
'/home/tbent/.local/include/python2.7'

chadgh · 2016-05-19T15:17:04Z

Yes I used pip to install
Arch Linux
Python 3.5.1
Virtualenv

>>> import pybind11
>>> pybind11.get_include()
'/home/chadgh/.pyenv/versions/3.5.1/include/python3.5m'
>>> pybind11.get_include(True)
'/home/chadgh/.local/include/python3.5m'

So maybe 3.5.1 is not supported?

tbenthompson · 2016-05-19T15:21:30Z

I use 3.5 for development, so that's not it.

Could you list the files in these folders?
/home/chadgh/.pyenv/versions/3.5.1/include/python3.5m/pybind11
/home/chadgh/.local/include/python3.5m/pybind11

chadgh · 2016-05-19T15:27:39Z

Those paths don't exist. I have /home/chadgh/.pyenv/versions/3.5.1/include/python3.5m/ but no pybind11 in there. And I have up to /home/chadgh/.local/ but no include.

I also did a search (using the find command) at those levels and didn't find anything called pybind11.

chadgh · 2016-05-19T15:28:37Z

In the virtualenvironment there is ./lib/python3.5/site-packages/pybind11 and ./include/site/python3.5/pybind11

tbenthompson · 2016-05-19T15:29:23Z

Want to list the files in ./include/site/python3.5/pybind11? I think pybind11 is getting confused about where it installed itself!

chadgh · 2016-05-19T15:31:41Z

Sure

attr.h
cast.h
common.h
complex.h
descr.h
functional.h
numpy.h
operators.h
pybind11.h
pytypes.h
stl.h
typeid.h

tbenthompson · 2016-05-19T15:39:24Z

Okay. So, it seems that pybind11 package installed the headers in ./include/site/python3.5 but pybind11.get_include(), which is supposed to return that directory, instead returns /home/chadgh/.pyenv/versions/3.5.1/include/python3.5m/. This is a problem with the pybind11 package.

Wenzel Jakob, who is the maintainer of that project, is usually pretty responsive. Would you be up for opening an issue there?

In the meantime, you can hack things to work properly by opening ./lib/python3.5/site-packages/pybind11/__init__.py and changing

return os.path.dirname(
            locations.distutils_scheme('pybind11', *args, **kwargs)['headers'])

to just have the hardcoded path where the pybind11/pybind11.h file is: In your case YOURVIRTUALENVPATHNAME/include/site.

chadgh · 2016-05-19T16:11:20Z

Hmm, @tbenthompson your suggestion didn't seem to work I replace the line you specified with:

return '/home/chadgh/.virtualenvs/tmp-2ea8e0bcd287cca/include/site/python3.5/pybind11'

And am getting the same error. I've confirmed that that is the location of the directory with all of the .h files.

Also, according to @wjakob this looks like it might be a pip issue. pypa/pip#3696

chadgh · 2016-05-19T16:14:11Z

I did just confirm that if I avoid the virtualenv, the example works.

tbenthompson · 2016-05-19T16:27:51Z

Glad we got to the root of the problem. Thanks for reporting this.

With your hack fix, the pybind11 at the end of the line is the problem. It should be:

return '/home/chadgh/.virtualenvs/tmp-2ea8e0bcd287cca/include/site/python3.5'

timbicker · 2019-04-23T07:11:20Z

I have the same problem with python 3.7.

tbenthompson · 2019-04-23T11:53:11Z

Did you read through the posts above? This would be a problem with the installation of pybind11, its interaction with pip and the function pybind11.get_include(). There's nothing cppimport can do to fix it, but if you read through the posts above, there's a hack of that function that would probably work for you. Also, you can go look here for what seems like the latest update on the odyssey of fixing this problem: pybind/pybind11#1190

jvines · 2019-05-10T18:47:27Z

Hi @timbicker ,

I mange to resolve this issue inside a virtualenv of python2.7 by installing pybind11 using conda install pybind11

Hope this helps

timbicker · 2019-05-10T19:14:45Z

Thanks for your help, I could solve the problem by doing the apt installs from the installation instruction.

simonhughes22 · 2019-10-09T22:13:36Z

Installing pybind11 with conda first fixed it for me, as per @jvines' suggestion

TeamATR · 2020-01-23T08:07:28Z

I got the same error when I tried to install scipy. Is this topic related? It has been raised in Dec 2019. I am wondering how it is going? Any clue now?

tbenthompson · 2020-01-24T15:13:03Z

That scipy issue does seem similar. You might find some useful information scrolling back through this issue and some of the other linked issues.

Adblu · 2020-03-16T12:31:23Z

Same issue here:

1.  pip to install
2. ubuntu 18.04
3. Python 3.6
4. Virtualenv

How to fix it ?

Adblu · 2020-03-16T12:40:29Z

Hi @timbicker ,

I mange to resolve this issue inside a virtualenv of python2.7 by installing pybind11 using conda install pybind11

Hope this helps

Thanks, it helped !

Abduhu · 2020-09-11T02:56:55Z

I had same problem. It seems that pip does not include pybind11 properly. Hence, I reinstalled pybind11 manully after cloning the package from github repository.
Resume: install pybind11 by pybind11/setup.py instead of pip of Pypi

tbenthompson · 2020-09-11T13:28:30Z

I had same problem. It seems that pip does not include pybind11 properly. Hence, I reinstalled pybind11 manully after cloning the package from github repository.
Resume: install pybind11 by pybind11/setup.py instead of pip of Pypi

It seems like the PyPI (pip) pybind11 package works for some people and not others. Have you tried the conda pybind11 package? That seems to consistently work, but obviously is useless if you're not using conda.

tanzhenyu · 2021-02-24T18:58:32Z

Hi @timbicker ,

I mange to resolve this issue inside a virtualenv of python2.7 by installing pybind11 using conda install pybind11

Hope this helps

I can confirm this works with python3.8 as well.

dman82499 · 2021-04-04T07:10:57Z

just confirmed the pip installation of pybind does not install the .h files for me as well, weird. Using windows with python 3.7.4. However, using pip install pybind11[global] fixed the issue for me.

tbenthompson · 2021-04-04T17:30:14Z

just confirmed the pip installation of pybind does not install the .h files for me as well, weird. Using windows with python 3.7.4. However, using pip install pybind11[global] fixed the issue for me.

Glad you got the issue resolved! You might leave post an issue to the pybind11 github issue tracker.

borgarpa · 2021-06-17T11:29:03Z

Hi @timbicker ,

I mange to resolve this issue inside a virtualenv of python2.7 by installing pybind11 using conda install pybind11

Hope this helps

It didn't work for me tho... I don't know why, but in my conda env it is just impossible for me to get pybind11 to work...

Full error prompt bellow:

Building wheel for torch-cluster (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/borgarpa/miniconda3/envs/torch-points_rocm/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uy795qau/torch-cluster_5100622c4e9142d2a68c48fb894edc3e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-uy795qau/torch-cluster_5100622c4e9142d2a68c48fb894edc3e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-ke6svzxy
       cwd: /tmp/pip-install-uy795qau/torch-cluster_5100622c4e9142d2a68c48fb894edc3e/
  Complete output (34 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.8
  creating build/lib.linux-x86_64-3.8/torch_cluster
  copying torch_cluster/nearest.py -> build/lib.linux-x86_64-3.8/torch_cluster
  copying torch_cluster/graclus.py -> build/lib.linux-x86_64-3.8/torch_cluster
  copying torch_cluster/__init__.py -> build/lib.linux-x86_64-3.8/torch_cluster
  copying torch_cluster/rw.py -> build/lib.linux-x86_64-3.8/torch_cluster
  copying torch_cluster/grid.py -> build/lib.linux-x86_64-3.8/torch_cluster
  copying torch_cluster/knn.py -> build/lib.linux-x86_64-3.8/torch_cluster
  copying torch_cluster/fps.py -> build/lib.linux-x86_64-3.8/torch_cluster
  copying torch_cluster/sampler.py -> build/lib.linux-x86_64-3.8/torch_cluster
  copying torch_cluster/radius.py -> build/lib.linux-x86_64-3.8/torch_cluster
  running build_ext
  building 'torch_cluster._sampler_cpu' extension
  creating build/temp.linux-x86_64-3.8
  creating build/temp.linux-x86_64-3.8/tmp
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-uy795qau
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-uy795qau/torch-cluster_5100622c4e9142d2a68c48fb894edc3e
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-uy795qau/torch-cluster_5100622c4e9142d2a68c48fb894edc3e/csrc
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-uy795qau/torch-cluster_5100622c4e9142d2a68c48fb894edc3e/csrc/cpu
  gcc -pthread -B /home/borgarpa/miniconda3/envs/torch-points_rocm/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-install-uy795qau/torch-cluster_5100622c4e9142d2a68c48fb894edc3e/csrc -I/home/borgarpa/miniconda3/envs/torch-points_rocm/lib/python3.8/site-packages/torch/include -I/home/borgarpa/miniconda3/envs/torch-points_rocm/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/borgarpa/miniconda3/envs/torch-points_rocm/lib/python3.8/site-packages/torch/include/TH -I/home/borgarpa/miniconda3/envs/torch-points_rocm/lib/python3.8/site-packages/torch/include/THC -I/home/borgarpa/miniconda3/envs/torch-points_rocm/include/python3.8 -c /tmp/pip-install-uy795qau/torch-cluster_5100622c4e9142d2a68c48fb894edc3e/csrc/sampler.cpp -o build/temp.linux-x86_64-3.8/tmp/pip-install-uy795qau/torch-cluster_5100622c4e9142d2a68c48fb894edc3e/csrc/sampler.o -fPIC -D__HIP_PLATFORM_HCC__=1 -O2 -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1013" -DTORCH_EXTENSION_NAME=_sampler_cpu -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++14
  cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
  In file included from /home/borgarpa/miniconda3/envs/torch-points_rocm/lib/python3.8/site-packages/torch/include/torch/csrc/api/include/torch/python.h:12,
                   from /home/borgarpa/miniconda3/envs/torch-points_rocm/lib/python3.8/site-packages/torch/include/torch/extension.h:6,
                   from /tmp/pip-install-uy795qau/torch-cluster_5100622c4e9142d2a68c48fb894edc3e/csrc/cpu/sampler_cpu.h:3,
                   from /tmp/pip-install-uy795qau/torch-cluster_5100622c4e9142d2a68c48fb894edc3e/csrc/sampler.cpp:4:
  /home/borgarpa/miniconda3/envs/torch-points_rocm/lib/python3.8/site-packages/torch/include/torch/csrc/utils/pybind.h:6:10: fatal error: pybind11/pybind11.h: No such file or directory
      6 | #include <pybind11/pybind11.h>
        |          ^~~~~~~~~~~~~~~~~~~~~
  compilation terminated.
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for torch-cluster

tbenthompson · 2021-06-18T20:33:43Z

Hi @borgarpa

I don't have a solution for you, but I just wanted to mention something that looks a bit funny to me. In the gcc command from your output, I don't see the pybind11 include directories being included with a -I. You might check the output of

import pybind11
pybind11.get_include()

That folder should show up in the gcc command.

For me, I get:

(cppimport) ➜  ~ python
Python 3.9.1 | packaged by conda-forge | (default, Jan 10 2021, 02:55:42)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybind11
>>> pybind11.get_include()
'/home/tbent/.miniconda3/envs/cppimport/lib/python3.9/site-packages/pybind11/include'

DSRajesh · 2024-01-26T09:05:04Z

Hi @borgarpa

I don't have a solution for you, but I just wanted to mention something that looks a bit funny to me. In the gcc command from your output, I don't see the pybind11 include directories being included with a -I. You might check the output of
import pybind11
pybind11.get_include()
That folder should show up in the gcc command.

For me, I get:
(cppimport) ➜  ~ python
Python 3.9.1 | packaged by conda-forge | (default, Jan 10 2021, 02:55:42)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybind11
>>> pybind11.get_include()
'/home/tbent/.miniconda3/envs/cppimport/lib/python3.9/site-packages/pybind11/include'

this worked for me. Thanks Mr. benthompson

tbenthompson self-assigned this May 19, 2016

chadgh mentioned this issue May 19, 2016

Trouble finding pybind11.h pybind/pybind11#201

Closed

tbenthompson closed this as completed May 19, 2016

sfarrens mentioned this issue May 2, 2019

[Installation issue]: python fails to build in a virtualenv due to pybind CEA-COSMIC/pysap#93

Closed

vladsterz mentioned this issue May 7, 2021

Could not load file or assembly Remote_eye_service.exe VCL3D/VolumetricCapture#53

Closed

borgarpa mentioned this issue Jun 17, 2021

fatal error: pybind11/pybind11.h: No such file or directory torch-points3d/torch-points3d#626

Closed

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fatal error: pybind11/pybind11.h: No such file or directory #2

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fatal error: pybind11/pybind11.h: No such file or directory #2

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