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J. Devez
Asked: 2018-02-19 11:34:48 +0800 CST

fatal error: Python.h: No such file or directory (Unsolved with python-devel)

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When trying to compile pycaffe on Ubuntu 16.04, with Anaconda 3.6 installed I get the following error:

python/caffe/_caffe.cpp:1:52: fatal error: Python.h: No such file or directory

I have tried to install the python-devel packages with

sudo apt-get install python3-dev 
sudo apt-get install python3.5-dev
sudo apt-get install python3.6-dev

But even after trying with each of those separately the same error occurs.

The correct PATH seems to be added in .bashrc

export PATH="home/jdevezas/anaconda/bin:$PATH"

And in Caffe's makefile.config I have 

# NOTE: this is required only if you will compile the python interface.
# We need to be able to find Python.h and numpy/arrayobject.h.
#PYTHON_INCLUDE := /usr/include/python2.7 \
        /usr/lib/python2.7/dist-packages/numpy/core/include
# Anaconda Python distribution is quite popular. Include path:
# Verify anaconda location, sometimes it's in root.

ANACONDA_HOME := /home/jdevezas/anaconda

#PYTHON_INCLUDE := $(ANACONDA_HOME)/include \
#            $(ANACONDA_HOME)/include/python2.7 \
#            $(ANACONDA_HOME)/lib/python2.7/site-packages/numpy/core/include

# Uncomment to use Python 3 (default is Python 2)
 PYTHON_LIBRARIES := boost_python3 python3.5m
 PYTHON_INCLUDE := /usr/include/python3.5m \
                 /usr/lib/python3.5/dist-packages/numpy/core/include

I have also tried with Python 2.7 with no results. I have checked the /usr/include/python3.5m and Python.h is there. Suggestions?

compiling python3 anaconda caffe

3 Answers

  1. Updated (2021-01-11): Python.h header is now in $CONDA_PREFIX/include/python3.Y (where Y is minor version) in case of Linux or $CONDA_PREFIX/include in Windows.

    Old answer: python.h header is in $CONDA_PREFIX/etc/include/python3.6m directory.

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  2. For tracking down the packages a file is in, use

    apt-file search Python.h

    The list (for Ubuntu 20.04) shows two likely candidates for the latest python version: libpython3.8-dev and pypy3-dev. The package you need to install is libpython3.8-dev

    Install apt-file with

    sudo apt-get install apt-file

    Then update its database:

    apt-file update
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  3. in my case the python folder was situated in /opt/anaconda3/include/, which I found by

    $ which conda
/opt/anaconda3/bin/conda

    the variable $CONDA_PREFIX was empty in my case, as

    $ echo $CONDA_PREFIX

    printed just an empty line.

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